Starting phenix.real_space_refine on Sun Mar 10 22:38:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oko_12963/03_2024/7oko_12963_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oko_12963/03_2024/7oko_12963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oko_12963/03_2024/7oko_12963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oko_12963/03_2024/7oko_12963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oko_12963/03_2024/7oko_12963_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oko_12963/03_2024/7oko_12963_neut.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 182 5.16 5 C 34424 2.51 5 N 9763 2.21 5 O 10114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "AA ARG 164": "NH1" <-> "NH2" Residue "AA ARG 187": "NH1" <-> "NH2" Residue "AB ARG 164": "NH1" <-> "NH2" Residue "AB ARG 187": "NH1" <-> "NH2" Residue "0 ARG 164": "NH1" <-> "NH2" Residue "0 ARG 187": "NH1" <-> "NH2" Residue "1 ARG 164": "NH1" <-> "NH2" Residue "1 ARG 187": "NH1" <-> "NH2" Residue "3 ARG 86": "NH1" <-> "NH2" Residue "3 GLU 110": "OE1" <-> "OE2" Residue "3 ARG 115": "NH1" <-> "NH2" Residue "3 GLU 120": "OE1" <-> "OE2" Residue "3 GLU 131": "OE1" <-> "OE2" Residue "3 GLU 137": "OE1" <-> "OE2" Residue "3 ARG 189": "NH1" <-> "NH2" Residue "3 ARG 193": "NH1" <-> "NH2" Residue "3 ARG 236": "NH1" <-> "NH2" Residue "4 ARG 86": "NH1" <-> "NH2" Residue "4 ARG 115": "NH1" <-> "NH2" Residue "4 GLU 131": "OE1" <-> "OE2" Residue "4 GLU 137": "OE1" <-> "OE2" Residue "4 GLU 158": "OE1" <-> "OE2" Residue "4 ARG 189": "NH1" <-> "NH2" Residue "4 ARG 193": "NH1" <-> "NH2" Residue "4 ARG 236": "NH1" <-> "NH2" Residue "5 ARG 164": "NH1" <-> "NH2" Residue "5 ARG 187": "NH1" <-> "NH2" Residue "6 ARG 164": "NH1" <-> "NH2" Residue "6 PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 187": "NH1" <-> "NH2" Residue "8 ARG 86": "NH1" <-> "NH2" Residue "8 GLU 110": "OE1" <-> "OE2" Residue "8 ARG 115": "NH1" <-> "NH2" Residue "8 GLU 131": "OE1" <-> "OE2" Residue "8 GLU 137": "OE1" <-> "OE2" Residue "8 ARG 189": "NH1" <-> "NH2" Residue "8 ARG 193": "NH1" <-> "NH2" Residue "8 ARG 236": "NH1" <-> "NH2" Residue "9 ARG 86": "NH1" <-> "NH2" Residue "9 ARG 115": "NH1" <-> "NH2" Residue "9 GLU 131": "OE1" <-> "OE2" Residue "9 GLU 137": "OE1" <-> "OE2" Residue "9 GLU 158": "OE1" <-> "OE2" Residue "9 ARG 189": "NH1" <-> "NH2" Residue "9 ARG 193": "NH1" <-> "NH2" Residue "9 ARG 236": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 193": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F GLU 131": "OE1" <-> "OE2" Residue "F GLU 137": "OE1" <-> "OE2" Residue "F ARG 189": "NH1" <-> "NH2" Residue "F ARG 193": "NH1" <-> "NH2" Residue "F ARG 236": "NH1" <-> "NH2" Residue "G ARG 86": "NH1" <-> "NH2" Residue "G ARG 115": "NH1" <-> "NH2" Residue "G GLU 131": "OE1" <-> "OE2" Residue "G GLU 137": "OE1" <-> "OE2" Residue "G GLU 158": "OE1" <-> "OE2" Residue "G ARG 189": "NH1" <-> "NH2" Residue "G ARG 193": "NH1" <-> "NH2" Residue "G ARG 236": "NH1" <-> "NH2" Residue "H ARG 164": "NH1" <-> "NH2" Residue "H ARG 187": "NH1" <-> "NH2" Residue "I ARG 164": "NH1" <-> "NH2" Residue "I ARG 187": "NH1" <-> "NH2" Residue "K ARG 86": "NH1" <-> "NH2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "K ARG 115": "NH1" <-> "NH2" Residue "K GLU 131": "OE1" <-> "OE2" Residue "K GLU 137": "OE1" <-> "OE2" Residue "K ARG 189": "NH1" <-> "NH2" Residue "K ARG 193": "NH1" <-> "NH2" Residue "K ARG 236": "NH1" <-> "NH2" Residue "L ARG 86": "NH1" <-> "NH2" Residue "L GLU 93": "OE1" <-> "OE2" Residue "L ARG 115": "NH1" <-> "NH2" Residue "L GLU 131": "OE1" <-> "OE2" Residue "L GLU 137": "OE1" <-> "OE2" Residue "L GLU 158": "OE1" <-> "OE2" Residue "L ARG 189": "NH1" <-> "NH2" Residue "L ARG 193": "NH1" <-> "NH2" Residue "L ARG 236": "NH1" <-> "NH2" Residue "M ARG 164": "NH1" <-> "NH2" Residue "M ARG 187": "NH1" <-> "NH2" Residue "N ARG 164": "NH1" <-> "NH2" Residue "N ARG 187": "NH1" <-> "NH2" Residue "P ARG 86": "NH1" <-> "NH2" Residue "P GLU 110": "OE1" <-> "OE2" Residue "P ARG 115": "NH1" <-> "NH2" Residue "P GLU 131": "OE1" <-> "OE2" Residue "P GLU 137": "OE1" <-> "OE2" Residue "P ARG 189": "NH1" <-> "NH2" Residue "P ARG 193": "NH1" <-> "NH2" Residue "P ARG 236": "NH1" <-> "NH2" Residue "Q ARG 86": "NH1" <-> "NH2" Residue "Q ARG 115": "NH1" <-> "NH2" Residue "Q GLU 131": "OE1" <-> "OE2" Residue "Q GLU 137": "OE1" <-> "OE2" Residue "Q GLU 158": "OE1" <-> "OE2" Residue "Q ARG 189": "NH1" <-> "NH2" Residue "Q ARG 193": "NH1" <-> "NH2" Residue "Q ARG 236": "NH1" <-> "NH2" Residue "R ARG 164": "NH1" <-> "NH2" Residue "R ARG 187": "NH1" <-> "NH2" Residue "S ARG 164": "NH1" <-> "NH2" Residue "S ARG 187": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U GLU 110": "OE1" <-> "OE2" Residue "U ARG 115": "NH1" <-> "NH2" Residue "U GLU 131": "OE1" <-> "OE2" Residue "U GLU 137": "OE1" <-> "OE2" Residue "U ARG 189": "NH1" <-> "NH2" Residue "U ARG 193": "NH1" <-> "NH2" Residue "U ARG 236": "NH1" <-> "NH2" Residue "V ARG 86": "NH1" <-> "NH2" Residue "V GLU 93": "OE1" <-> "OE2" Residue "V ARG 115": "NH1" <-> "NH2" Residue "V GLU 131": "OE1" <-> "OE2" Residue "V GLU 137": "OE1" <-> "OE2" Residue "V GLU 158": "OE1" <-> "OE2" Residue "V ARG 189": "NH1" <-> "NH2" Residue "V ARG 193": "NH1" <-> "NH2" Residue "V ARG 236": "NH1" <-> "NH2" Residue "W ARG 164": "NH1" <-> "NH2" Residue "W ARG 187": "NH1" <-> "NH2" Residue "X ARG 164": "NH1" <-> "NH2" Residue "X ARG 187": "NH1" <-> "NH2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z GLU 110": "OE1" <-> "OE2" Residue "Z ARG 115": "NH1" <-> "NH2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z GLU 137": "OE1" <-> "OE2" Residue "Z ARG 189": "NH1" <-> "NH2" Residue "Z ARG 193": "NH1" <-> "NH2" Residue "Z GLU 204": "OE1" <-> "OE2" Residue "Z ARG 236": "NH1" <-> "NH2" Residue "a ARG 86": "NH1" <-> "NH2" Residue "a PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 115": "NH1" <-> "NH2" Residue "a GLU 131": "OE1" <-> "OE2" Residue "a GLU 137": "OE1" <-> "OE2" Residue "a GLU 158": "OE1" <-> "OE2" Residue "a ARG 189": "NH1" <-> "NH2" Residue "a ARG 193": "NH1" <-> "NH2" Residue "a ARG 236": "NH1" <-> "NH2" Residue "b ARG 164": "NH1" <-> "NH2" Residue "b ARG 187": "NH1" <-> "NH2" Residue "c ARG 164": "NH1" <-> "NH2" Residue "c ARG 187": "NH1" <-> "NH2" Residue "e ARG 86": "NH1" <-> "NH2" Residue "e GLU 110": "OE1" <-> "OE2" Residue "e ARG 115": "NH1" <-> "NH2" Residue "e GLU 131": "OE1" <-> "OE2" Residue "e GLU 137": "OE1" <-> "OE2" Residue "e ARG 189": "NH1" <-> "NH2" Residue "e ARG 193": "NH1" <-> "NH2" Residue "e GLU 204": "OE1" <-> "OE2" Residue "e ARG 236": "NH1" <-> "NH2" Residue "f ARG 86": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f GLU 131": "OE1" <-> "OE2" Residue "f GLU 137": "OE1" <-> "OE2" Residue "f GLU 158": "OE1" <-> "OE2" Residue "f ARG 189": "NH1" <-> "NH2" Residue "f ARG 193": "NH1" <-> "NH2" Residue "f ARG 236": "NH1" <-> "NH2" Residue "g ARG 164": "NH1" <-> "NH2" Residue "g ARG 187": "NH1" <-> "NH2" Residue "h ARG 164": "NH1" <-> "NH2" Residue "h ARG 187": "NH1" <-> "NH2" Residue "j ARG 86": "NH1" <-> "NH2" Residue "j GLU 110": "OE1" <-> "OE2" Residue "j ARG 115": "NH1" <-> "NH2" Residue "j GLU 131": "OE1" <-> "OE2" Residue "j GLU 137": "OE1" <-> "OE2" Residue "j GLU 158": "OE1" <-> "OE2" Residue "j ARG 189": "NH1" <-> "NH2" Residue "j ARG 193": "NH1" <-> "NH2" Residue "j ARG 236": "NH1" <-> "NH2" Residue "k ARG 86": "NH1" <-> "NH2" Residue "k GLU 93": "OE1" <-> "OE2" Residue "k ARG 115": "NH1" <-> "NH2" Residue "k GLU 131": "OE1" <-> "OE2" Residue "k GLU 137": "OE1" <-> "OE2" Residue "k GLU 158": "OE1" <-> "OE2" Residue "k ARG 189": "NH1" <-> "NH2" Residue "k ARG 193": "NH1" <-> "NH2" Residue "k ARG 236": "NH1" <-> "NH2" Residue "l ARG 164": "NH1" <-> "NH2" Residue "l ARG 187": "NH1" <-> "NH2" Residue "m ARG 164": "NH1" <-> "NH2" Residue "m ARG 187": "NH1" <-> "NH2" Residue "o ARG 86": "NH1" <-> "NH2" Residue "o GLU 110": "OE1" <-> "OE2" Residue "o ARG 115": "NH1" <-> "NH2" Residue "o GLU 131": "OE1" <-> "OE2" Residue "o GLU 137": "OE1" <-> "OE2" Residue "o ARG 189": "NH1" <-> "NH2" Residue "o ARG 193": "NH1" <-> "NH2" Residue "o ARG 236": "NH1" <-> "NH2" Residue "p ARG 86": "NH1" <-> "NH2" Residue "p GLU 110": "OE1" <-> "OE2" Residue "p ARG 115": "NH1" <-> "NH2" Residue "p GLU 131": "OE1" <-> "OE2" Residue "p GLU 137": "OE1" <-> "OE2" Residue "p GLU 158": "OE1" <-> "OE2" Residue "p ARG 189": "NH1" <-> "NH2" Residue "p ARG 193": "NH1" <-> "NH2" Residue "p ARG 236": "NH1" <-> "NH2" Residue "q ARG 164": "NH1" <-> "NH2" Residue "q ARG 187": "NH1" <-> "NH2" Residue "r ARG 164": "NH1" <-> "NH2" Residue "r ARG 187": "NH1" <-> "NH2" Residue "t ARG 86": "NH1" <-> "NH2" Residue "t GLU 110": "OE1" <-> "OE2" Residue "t ARG 115": "NH1" <-> "NH2" Residue "t GLU 131": "OE1" <-> "OE2" Residue "t GLU 137": "OE1" <-> "OE2" Residue "t GLU 158": "OE1" <-> "OE2" Residue "t ARG 189": "NH1" <-> "NH2" Residue "t ARG 193": "NH1" <-> "NH2" Residue "t ARG 236": "NH1" <-> "NH2" Residue "u ARG 86": "NH1" <-> "NH2" Residue "u ARG 115": "NH1" <-> "NH2" Residue "u GLU 131": "OE1" <-> "OE2" Residue "u GLU 137": "OE1" <-> "OE2" Residue "u GLU 158": "OE1" <-> "OE2" Residue "u ARG 189": "NH1" <-> "NH2" Residue "u ARG 193": "NH1" <-> "NH2" Residue "u ARG 236": "NH1" <-> "NH2" Residue "v ARG 164": "NH1" <-> "NH2" Residue "v ARG 187": "NH1" <-> "NH2" Residue "w ARG 164": "NH1" <-> "NH2" Residue "w ARG 187": "NH1" <-> "NH2" Residue "y ARG 86": "NH1" <-> "NH2" Residue "y GLU 110": "OE1" <-> "OE2" Residue "y ARG 115": "NH1" <-> "NH2" Residue "y GLU 131": "OE1" <-> "OE2" Residue "y GLU 137": "OE1" <-> "OE2" Residue "y ARG 189": "NH1" <-> "NH2" Residue "y ARG 193": "NH1" <-> "NH2" Residue "y ARG 236": "NH1" <-> "NH2" Residue "z ARG 86": "NH1" <-> "NH2" Residue "z GLU 110": "OE1" <-> "OE2" Residue "z ARG 115": "NH1" <-> "NH2" Residue "z GLU 131": "OE1" <-> "OE2" Residue "z GLU 137": "OE1" <-> "OE2" Residue "z GLU 158": "OE1" <-> "OE2" Residue "z ARG 189": "NH1" <-> "NH2" Residue "z ARG 193": "NH1" <-> "NH2" Residue "z ARG 236": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 54483 Number of models: 1 Model: "" Number of chains: 65 Chain: "AA" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "AB" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "AC" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "0" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "1" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "2" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "3" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "4" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "5" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "6" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "7" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "8" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "9" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "A" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "B" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "C" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "D" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "E" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "F" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "G" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "H" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "I" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "J" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "K" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "L" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "M" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "N" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "O" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "P" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "Q" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "R" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "S" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "T" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "U" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "V" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "W" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "X" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "Y" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "Z" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "a" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "b" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "c" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "d" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "e" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "f" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "g" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "h" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "i" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "j" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "k" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "l" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "m" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "n" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "o" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "p" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "q" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "r" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "s" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "t" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "u" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "v" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "w" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "x" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "y" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "z" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Time building chain proxies: 20.06, per 1000 atoms: 0.37 Number of scatterers: 54483 At special positions: 0 Unit cell: (277.2, 278.3, 112.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 182 16.00 O 10114 8.00 N 9763 7.00 C 34424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.32 Conformation dependent library (CDL) restraints added in 7.2 seconds 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12922 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 6.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain '3' and resid 125 through 133 Processing helix chain '3' and resid 136 through 149 Processing helix chain '4' and resid 137 through 147 Processing helix chain '4' and resid 149 through 149 No H-bonds generated for 'chain '4' and resid 149 through 149' Processing helix chain '9' and resid 137 through 147 Processing helix chain '9' and resid 149 through 149 No H-bonds generated for 'chain '9' and resid 149 through 149' Processing helix chain '8' and resid 125 through 133 Processing helix chain '8' and resid 136 through 149 Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'B' and resid 137 through 147 Processing helix chain 'B' and resid 149 through 149 No H-bonds generated for 'chain 'B' and resid 149 through 149' Processing helix chain 'G' and resid 137 through 147 Processing helix chain 'G' and resid 149 through 149 No H-bonds generated for 'chain 'G' and resid 149 through 149' Processing helix chain 'F' and resid 125 through 133 Processing helix chain 'F' and resid 136 through 149 Processing helix chain 'K' and resid 125 through 133 Processing helix chain 'K' and resid 136 through 149 Processing helix chain 'L' and resid 137 through 147 Processing helix chain 'L' and resid 149 through 149 No H-bonds generated for 'chain 'L' and resid 149 through 149' Processing helix chain 'Q' and resid 137 through 147 Processing helix chain 'Q' and resid 149 through 149 No H-bonds generated for 'chain 'Q' and resid 149 through 149' Processing helix chain 'P' and resid 125 through 133 Processing helix chain 'P' and resid 136 through 149 Processing helix chain 'U' and resid 125 through 133 Processing helix chain 'U' and resid 136 through 149 Processing helix chain 'V' and resid 137 through 147 Processing helix chain 'V' and resid 149 through 149 No H-bonds generated for 'chain 'V' and resid 149 through 149' Processing helix chain 'Z' and resid 125 through 133 Processing helix chain 'Z' and resid 136 through 149 Processing helix chain 'a' and resid 137 through 147 Processing helix chain 'a' and resid 149 through 149 No H-bonds generated for 'chain 'a' and resid 149 through 149' Processing helix chain 'e' and resid 125 through 133 Processing helix chain 'e' and resid 136 through 149 Processing helix chain 'f' and resid 137 through 147 Processing helix chain 'f' and resid 149 through 149 No H-bonds generated for 'chain 'f' and resid 149 through 149' Processing helix chain 'k' and resid 137 through 147 Processing helix chain 'k' and resid 149 through 149 No H-bonds generated for 'chain 'k' and resid 149 through 149' Processing helix chain 'j' and resid 125 through 133 Processing helix chain 'j' and resid 136 through 149 Processing helix chain 'o' and resid 125 through 133 Processing helix chain 'o' and resid 136 through 149 Processing helix chain 'p' and resid 137 through 147 Processing helix chain 'p' and resid 149 through 149 No H-bonds generated for 'chain 'p' and resid 149 through 149' Processing helix chain 'u' and resid 137 through 147 Processing helix chain 'u' and resid 149 through 149 No H-bonds generated for 'chain 'u' and resid 149 through 149' Processing helix chain 't' and resid 125 through 133 Processing helix chain 't' and resid 136 through 149 Processing helix chain 'y' and resid 125 through 133 Processing helix chain 'y' and resid 136 through 149 Processing helix chain 'z' and resid 137 through 147 Processing helix chain 'z' and resid 149 through 149 No H-bonds generated for 'chain 'z' and resid 149 through 149' 286 hydrogen bonds defined for protein. 858 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.25 Time building geometry restraints manager: 17.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 8994 1.31 - 1.44: 14823 1.44 - 1.57: 31563 1.57 - 1.69: 0 1.69 - 1.82: 364 Bond restraints: 55744 Sorted by residual: bond pdb=" C PRO c 185 " pdb=" O PRO c 185 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.19e-02 7.06e+03 1.35e+01 bond pdb=" C PRO I 185 " pdb=" O PRO I 185 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.19e-02 7.06e+03 1.34e+01 bond pdb=" C PRO X 185 " pdb=" O PRO X 185 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.23e-02 6.61e+03 1.28e+01 bond pdb=" N GLY c 186 " pdb=" CA GLY c 186 " ideal model delta sigma weight residual 1.447 1.480 -0.034 1.01e-02 9.80e+03 1.12e+01 bond pdb=" C VAL 4 212 " pdb=" O VAL 4 212 " ideal model delta sigma weight residual 1.237 1.206 0.031 9.80e-03 1.04e+04 1.02e+01 ... (remaining 55739 not shown) Histogram of bond angle deviations from ideal: 94.10 - 102.12: 229 102.12 - 110.15: 12739 110.15 - 118.18: 30302 118.18 - 126.20: 31343 126.20 - 134.23: 1294 Bond angle restraints: 75907 Sorted by residual: angle pdb=" C PHE X 182 " pdb=" CA PHE X 182 " pdb=" CB PHE X 182 " ideal model delta sigma weight residual 110.77 94.10 16.67 1.67e+00 3.59e-01 9.97e+01 angle pdb=" C PHE I 182 " pdb=" CA PHE I 182 " pdb=" CB PHE I 182 " ideal model delta sigma weight residual 110.29 98.58 11.71 1.64e+00 3.72e-01 5.10e+01 angle pdb=" CA PHE X 182 " pdb=" C PHE X 182 " pdb=" O PHE X 182 " ideal model delta sigma weight residual 120.60 112.56 8.04 1.13e+00 7.83e-01 5.06e+01 angle pdb=" CA GLYAA 186 " pdb=" C GLYAA 186 " pdb=" O GLYAA 186 " ideal model delta sigma weight residual 121.38 115.46 5.92 9.40e-01 1.13e+00 3.97e+01 angle pdb=" CA GLY X 186 " pdb=" C GLY X 186 " pdb=" O GLY X 186 " ideal model delta sigma weight residual 121.38 115.50 5.88 9.40e-01 1.13e+00 3.92e+01 ... (remaining 75902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 30174 17.84 - 35.68: 2553 35.68 - 53.52: 326 53.52 - 71.36: 106 71.36 - 89.20: 43 Dihedral angle restraints: 33202 sinusoidal: 13130 harmonic: 20072 Sorted by residual: dihedral pdb=" C PHE X 182 " pdb=" N PHE X 182 " pdb=" CA PHE X 182 " pdb=" CB PHE X 182 " ideal model delta harmonic sigma weight residual -122.60 -100.46 -22.14 0 2.50e+00 1.60e-01 7.84e+01 dihedral pdb=" C PHE I 182 " pdb=" N PHE I 182 " pdb=" CA PHE I 182 " pdb=" CB PHE I 182 " ideal model delta harmonic sigma weight residual -122.60 -105.34 -17.26 0 2.50e+00 1.60e-01 4.77e+01 dihedral pdb=" C PHE m 182 " pdb=" N PHE m 182 " pdb=" CA PHE m 182 " pdb=" CB PHE m 182 " ideal model delta harmonic sigma weight residual -122.60 -110.06 -12.54 0 2.50e+00 1.60e-01 2.52e+01 ... (remaining 33199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 7926 0.094 - 0.187: 554 0.187 - 0.281: 13 0.281 - 0.374: 19 0.374 - 0.468: 3 Chirality restraints: 8515 Sorted by residual: chirality pdb=" CA PHE X 182 " pdb=" N PHE X 182 " pdb=" C PHE X 182 " pdb=" CB PHE X 182 " both_signs ideal model delta sigma weight residual False 2.51 2.98 -0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" CA PHE I 182 " pdb=" N PHE I 182 " pdb=" C PHE I 182 " pdb=" CB PHE I 182 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CA ASN r 180 " pdb=" N ASN r 180 " pdb=" C ASN r 180 " pdb=" CB ASN r 180 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.97e+00 ... (remaining 8512 not shown) Planarity restraints: 9919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP e 46 " 0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO e 47 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO e 47 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO e 47 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA k 62 " 0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO k 63 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO k 63 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO k 63 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP y 46 " 0.054 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO y 47 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO y 47 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO y 47 " 0.044 5.00e-02 4.00e+02 ... (remaining 9916 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 581 2.59 - 3.17: 46276 3.17 - 3.74: 77741 3.74 - 4.32: 104244 4.32 - 4.90: 180701 Nonbonded interactions: 409543 Sorted by model distance: nonbonded pdb=" OD1 ASN I 180 " pdb=" NE1 TRP S 197 " model vdw 2.010 2.520 nonbonded pdb=" OG1 THR L 149 " pdb=" OD1 ASP L 151 " model vdw 2.085 2.440 nonbonded pdb=" OG1 THR 4 149 " pdb=" OD1 ASP 4 151 " model vdw 2.087 2.440 nonbonded pdb=" OG1 THR u 149 " pdb=" OD1 ASP u 151 " model vdw 2.117 2.440 nonbonded pdb=" OD2 ASP A 218 " pdb=" OG1 THR A 231 " model vdw 2.126 2.440 ... (remaining 409538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '5' selection = chain 'AB' selection = chain 'C' selection = chain 'H' selection = chain 'M' selection = chain 'R' selection = chain 'W' selection = chain 'b' selection = chain 'g' selection = chain 'l' selection = chain 'q' selection = chain 'v' } ncs_group { reference = chain '1' selection = chain '6' selection = chain 'AA' selection = chain 'D' selection = chain 'I' selection = chain 'N' selection = chain 'S' selection = chain 'X' selection = chain 'c' selection = chain 'h' selection = chain 'm' selection = chain 'r' selection = chain 'w' } ncs_group { reference = chain '2' selection = chain '7' selection = chain 'AC' selection = chain 'E' selection = chain 'J' selection = chain 'O' selection = chain 'T' selection = chain 'Y' selection = chain 'd' selection = chain 'i' selection = chain 'n' selection = chain 's' selection = chain 'x' } ncs_group { reference = chain '3' selection = chain '4' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'B' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'L' selection = chain 'P' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'j' selection = chain 'k' selection = chain 'o' selection = chain 'p' selection = chain 't' selection = chain 'u' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 25.870 Check model and map are aligned: 0.610 Set scattering table: 0.380 Process input model: 95.900 Find NCS groups from input model: 3.420 Set up NCS constraints: 0.900 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 55744 Z= 0.390 Angle : 0.835 16.674 75907 Z= 0.483 Chirality : 0.051 0.468 8515 Planarity : 0.007 0.086 9919 Dihedral : 13.642 89.202 20280 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.35 % Favored : 85.49 % Rotamer: Outliers : 0.92 % Allowed : 1.42 % Favored : 97.66 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.09), residues: 6968 helix: -1.28 (0.20), residues: 507 sheet: -2.13 (0.11), residues: 2028 loop : -2.86 (0.09), residues: 4433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 208 HIS 0.009 0.002 HIS I 183 PHE 0.027 0.002 PHE c 182 TYR 0.023 0.002 TYR L 136 ARG 0.016 0.001 ARG e 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1516 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1463 time to evaluate : 4.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 180 ASN cc_start: 0.8454 (t0) cc_final: 0.8004 (t0) REVERT: 0 180 ASN cc_start: 0.8570 (t0) cc_final: 0.8132 (t0) REVERT: 4 66 MET cc_start: 0.5857 (mmt) cc_final: 0.5419 (mmt) REVERT: 4 85 THR cc_start: 0.8076 (p) cc_final: 0.7787 (t) REVERT: 4 166 ILE cc_start: 0.7269 (pt) cc_final: 0.6621 (pt) REVERT: 5 180 ASN cc_start: 0.8383 (t0) cc_final: 0.8144 (t0) REVERT: 8 128 ARG cc_start: 0.7903 (tpp80) cc_final: 0.7526 (tpp80) REVERT: 9 191 GLU cc_start: 0.5698 (tm-30) cc_final: 0.5469 (tm-30) REVERT: B 66 MET cc_start: 0.6722 (mmt) cc_final: 0.6142 (mmp) REVERT: C 180 ASN cc_start: 0.8514 (t0) cc_final: 0.7966 (t0) REVERT: F 128 ARG cc_start: 0.8109 (tpp80) cc_final: 0.7824 (tpp80) REVERT: H 177 ASP cc_start: 0.7580 (t0) cc_final: 0.7346 (t0) REVERT: K 151 ASP cc_start: 0.6995 (p0) cc_final: 0.6761 (p0) REVERT: L 58 THR cc_start: 0.8837 (m) cc_final: 0.8607 (p) REVERT: L 117 MET cc_start: 0.7108 (ptm) cc_final: 0.6854 (ptm) REVERT: M 180 ASN cc_start: 0.8130 (t0) cc_final: 0.7565 (t0) REVERT: Q 191 GLU cc_start: 0.6003 (tm-30) cc_final: 0.5780 (tm-30) REVERT: R 180 ASN cc_start: 0.8523 (t0) cc_final: 0.7969 (t0) REVERT: U 151 ASP cc_start: 0.7161 (p0) cc_final: 0.6775 (p0) REVERT: V 66 MET cc_start: 0.6292 (mmt) cc_final: 0.5792 (mmt) REVERT: V 85 THR cc_start: 0.8038 (p) cc_final: 0.7757 (t) REVERT: b 157 THR cc_start: 0.6591 (p) cc_final: 0.6216 (p) REVERT: f 85 THR cc_start: 0.7930 (p) cc_final: 0.7494 (t) REVERT: f 191 GLU cc_start: 0.5931 (tm-30) cc_final: 0.5610 (tm-30) REVERT: l 180 ASN cc_start: 0.8837 (t0) cc_final: 0.8515 (t0) REVERT: o 110 GLU cc_start: 0.6581 (tt0) cc_final: 0.6367 (tt0) REVERT: o 235 ILE cc_start: 0.9118 (mm) cc_final: 0.8880 (mm) REVERT: p 85 THR cc_start: 0.7782 (p) cc_final: 0.7472 (t) REVERT: r 179 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6369 (p0) REVERT: y 66 MET cc_start: 0.7808 (mmp) cc_final: 0.6982 (mmp) REVERT: y 163 SER cc_start: 0.8010 (p) cc_final: 0.7780 (t) outliers start: 53 outliers final: 35 residues processed: 1476 average time/residue: 0.4964 time to fit residues: 1225.8209 Evaluate side-chains 1221 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1185 time to evaluate : 4.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 179 ASP Chi-restraints excluded: chain AA residue 188 VAL Chi-restraints excluded: chain AA residue 199 LEU Chi-restraints excluded: chain 1 residue 166 GLN Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 1 residue 199 LEU Chi-restraints excluded: chain 4 residue 210 PRO Chi-restraints excluded: chain 6 residue 179 ASP Chi-restraints excluded: chain 6 residue 188 VAL Chi-restraints excluded: chain 6 residue 199 LEU Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain I residue 166 GLN Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain S residue 166 GLN Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 188 VAL Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain X residue 166 GLN Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain c residue 166 GLN Chi-restraints excluded: chain h residue 166 GLN Chi-restraints excluded: chain h residue 179 ASP Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain m residue 166 GLN Chi-restraints excluded: chain m residue 179 ASP Chi-restraints excluded: chain m residue 188 VAL Chi-restraints excluded: chain r residue 179 ASP Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain w residue 179 ASP Chi-restraints excluded: chain w residue 188 VAL Chi-restraints excluded: chain w residue 199 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 689 random chunks: chunk 581 optimal weight: 3.9990 chunk 522 optimal weight: 5.9990 chunk 289 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 352 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 540 optimal weight: 0.0970 chunk 208 optimal weight: 9.9990 chunk 328 optimal weight: 3.9990 chunk 401 optimal weight: 5.9990 chunk 625 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 238 ASN ** 4 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 37 GLN 8 134 GLN 9 48 ASN ** 9 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 37 GLN A 134 GLN ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 134 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 180 ASN N 184 GLN P 37 GLN ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 159 HIS Z 37 GLN Z 144 ASN ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 184 GLN e 37 GLN f 48 ASN f 144 ASN f 184 GLN h 184 GLN j 37 GLN j 184 GLN ** k 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 184 GLN o 37 GLN o 134 GLN p 184 GLN ** r 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 184 GLN y 37 GLN y 134 GLN z 48 ASN ** z 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 55744 Z= 0.370 Angle : 0.714 9.441 75907 Z= 0.364 Chirality : 0.046 0.192 8515 Planarity : 0.007 0.079 9919 Dihedral : 6.041 65.452 7768 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.42 % Favored : 85.58 % Rotamer: Outliers : 3.50 % Allowed : 14.29 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.09), residues: 6968 helix: -1.87 (0.18), residues: 624 sheet: -2.26 (0.11), residues: 2171 loop : -2.82 (0.09), residues: 4173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP V 130 HIS 0.008 0.002 HIS r 159 PHE 0.018 0.002 PHE 3 88 TYR 0.024 0.002 TYR Q 136 ARG 0.009 0.001 ARG 4 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1462 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1260 time to evaluate : 4.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AA 180 ASN cc_start: 0.7475 (m-40) cc_final: 0.7224 (p0) REVERT: AA 199 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7814 (mm) REVERT: AB 180 ASN cc_start: 0.8610 (t0) cc_final: 0.8256 (t0) REVERT: 0 177 ASP cc_start: 0.7308 (t0) cc_final: 0.6952 (t0) REVERT: 0 180 ASN cc_start: 0.8550 (t0) cc_final: 0.8229 (t0) REVERT: 4 66 MET cc_start: 0.6584 (mmt) cc_final: 0.5844 (mmp) REVERT: 4 85 THR cc_start: 0.8051 (p) cc_final: 0.7820 (t) REVERT: 4 191 GLU cc_start: 0.5992 (tm-30) cc_final: 0.5596 (tm-30) REVERT: 5 180 ASN cc_start: 0.8444 (t0) cc_final: 0.8201 (t0) REVERT: 6 199 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7658 (mm) REVERT: 9 63 PRO cc_start: 0.7719 (Cg_endo) cc_final: 0.7469 (Cg_exo) REVERT: 9 191 GLU cc_start: 0.5734 (tm-30) cc_final: 0.5488 (tm-30) REVERT: A 138 LYS cc_start: 0.8301 (ptmt) cc_final: 0.8029 (tttt) REVERT: A 164 ASP cc_start: 0.7382 (p0) cc_final: 0.7177 (p0) REVERT: B 66 MET cc_start: 0.6791 (mmt) cc_final: 0.5999 (mmp) REVERT: B 188 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7330 (m-30) REVERT: C 180 ASN cc_start: 0.8629 (t0) cc_final: 0.8188 (t0) REVERT: G 63 PRO cc_start: 0.8117 (Cg_exo) cc_final: 0.7607 (Cg_endo) REVERT: G 85 THR cc_start: 0.7822 (OUTLIER) cc_final: 0.7603 (t) REVERT: I 199 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7975 (mm) REVERT: K 66 MET cc_start: 0.7442 (mmp) cc_final: 0.7082 (mmp) REVERT: K 151 ASP cc_start: 0.7089 (p0) cc_final: 0.6799 (p0) REVERT: L 85 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7653 (t) REVERT: L 90 ILE cc_start: 0.8891 (mt) cc_final: 0.8688 (mt) REVERT: L 117 MET cc_start: 0.7212 (ptm) cc_final: 0.6970 (ptm) REVERT: L 144 ASN cc_start: 0.8476 (t0) cc_final: 0.8109 (t0) REVERT: L 191 GLU cc_start: 0.5982 (tm-30) cc_final: 0.5281 (tm-30) REVERT: L 192 LEU cc_start: 0.6914 (mp) cc_final: 0.6467 (tp) REVERT: M 180 ASN cc_start: 0.8218 (t0) cc_final: 0.7787 (t0) REVERT: N 199 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7469 (mm) REVERT: Q 66 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6694 (mmp) REVERT: Q 144 ASN cc_start: 0.8530 (t0) cc_final: 0.8281 (t0) REVERT: Q 191 GLU cc_start: 0.5970 (tm-30) cc_final: 0.5725 (tm-30) REVERT: R 180 ASN cc_start: 0.8613 (t0) cc_final: 0.8220 (t0) REVERT: U 128 ARG cc_start: 0.8100 (tpp80) cc_final: 0.7624 (tpp80) REVERT: U 151 ASP cc_start: 0.7244 (p0) cc_final: 0.6817 (p0) REVERT: V 85 THR cc_start: 0.7987 (p) cc_final: 0.7725 (t) REVERT: V 144 ASN cc_start: 0.8595 (t0) cc_final: 0.8385 (t0) REVERT: b 157 THR cc_start: 0.6669 (OUTLIER) cc_final: 0.6215 (m) REVERT: f 63 PRO cc_start: 0.7510 (Cg_endo) cc_final: 0.7217 (Cg_exo) REVERT: f 85 THR cc_start: 0.7912 (p) cc_final: 0.7625 (t) REVERT: l 180 ASN cc_start: 0.8701 (t0) cc_final: 0.8418 (t0) REVERT: m 177 ASP cc_start: 0.8032 (t0) cc_final: 0.7798 (t0) REVERT: o 235 ILE cc_start: 0.9089 (mm) cc_final: 0.8872 (mm) REVERT: u 85 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7704 (t) REVERT: u 191 GLU cc_start: 0.6033 (tm-30) cc_final: 0.5670 (tm-30) REVERT: v 74 GLU cc_start: 0.7709 (mp0) cc_final: 0.7276 (mp0) REVERT: w 199 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7222 (mm) REVERT: z 144 ASN cc_start: 0.8464 (t0) cc_final: 0.8198 (t0) outliers start: 202 outliers final: 112 residues processed: 1339 average time/residue: 0.4971 time to fit residues: 1124.5866 Evaluate side-chains 1315 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1192 time to evaluate : 4.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain AA residue 188 VAL Chi-restraints excluded: chain AA residue 199 LEU Chi-restraints excluded: chain AB residue 191 VAL Chi-restraints excluded: chain AC residue 181 ASP Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 1 residue 198 VAL Chi-restraints excluded: chain 2 residue 181 ASP Chi-restraints excluded: chain 3 residue 30 ILE Chi-restraints excluded: chain 3 residue 46 ASP Chi-restraints excluded: chain 4 residue 175 THR Chi-restraints excluded: chain 5 residue 74 GLU Chi-restraints excluded: chain 6 residue 179 ASP Chi-restraints excluded: chain 6 residue 188 VAL Chi-restraints excluded: chain 6 residue 199 LEU Chi-restraints excluded: chain 7 residue 181 ASP Chi-restraints excluded: chain 8 residue 46 ASP Chi-restraints excluded: chain 8 residue 163 SER Chi-restraints excluded: chain 8 residue 188 ASP Chi-restraints excluded: chain 9 residue 48 ASN Chi-restraints excluded: chain 9 residue 175 THR Chi-restraints excluded: chain 9 residue 204 GLU Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 138 LYS Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 145 ARG Chi-restraints excluded: chain P residue 163 SER Chi-restraints excluded: chain Q residue 48 ASN Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 159 HIS Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain W residue 167 ILE Chi-restraints excluded: chain X residue 179 ASP Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Z residue 145 ARG Chi-restraints excluded: chain Z residue 163 SER Chi-restraints excluded: chain Z residue 220 ASN Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 223 THR Chi-restraints excluded: chain b residue 157 THR Chi-restraints excluded: chain b residue 188 VAL Chi-restraints excluded: chain d residue 181 ASP Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 163 SER Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 175 THR Chi-restraints excluded: chain f residue 204 GLU Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain h residue 179 ASP Chi-restraints excluded: chain j residue 46 ASP Chi-restraints excluded: chain j residue 92 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 173 SER Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain m residue 179 ASP Chi-restraints excluded: chain n residue 181 ASP Chi-restraints excluded: chain o residue 141 ILE Chi-restraints excluded: chain o residue 163 SER Chi-restraints excluded: chain o residue 188 ASP Chi-restraints excluded: chain p residue 48 ASN Chi-restraints excluded: chain p residue 173 SER Chi-restraints excluded: chain p residue 175 THR Chi-restraints excluded: chain q residue 73 VAL Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain q residue 191 VAL Chi-restraints excluded: chain t residue 46 ASP Chi-restraints excluded: chain u residue 85 THR Chi-restraints excluded: chain u residue 175 THR Chi-restraints excluded: chain w residue 179 ASP Chi-restraints excluded: chain w residue 188 VAL Chi-restraints excluded: chain w residue 199 LEU Chi-restraints excluded: chain y residue 46 ASP Chi-restraints excluded: chain y residue 117 MET Chi-restraints excluded: chain y residue 134 GLN Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 143 LEU Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 175 THR Chi-restraints excluded: chain z residue 204 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 689 random chunks: chunk 347 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 520 optimal weight: 6.9990 chunk 426 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 626 optimal weight: 3.9990 chunk 677 optimal weight: 0.9990 chunk 558 optimal weight: 0.0170 chunk 621 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 502 optimal weight: 6.9990 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 134 GLN ** 9 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN F 222 GLN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 ASN U 134 GLN ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 180 ASN j 134 GLN ** k 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 134 GLN q 159 HIS ** r 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 48 ASN z 144 ASN ** z 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 55744 Z= 0.211 Angle : 0.624 10.200 75907 Z= 0.312 Chirality : 0.044 0.215 8515 Planarity : 0.006 0.078 9919 Dihedral : 5.077 58.249 7730 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 2.75 % Allowed : 18.09 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.10), residues: 6968 helix: -1.48 (0.18), residues: 624 sheet: -1.99 (0.11), residues: 2236 loop : -2.57 (0.09), residues: 4108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 4 208 HIS 0.004 0.001 HIS q 159 PHE 0.013 0.001 PHE t 38 TYR 0.011 0.001 TYR a 136 ARG 0.005 0.000 ARG o 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1387 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1228 time to evaluate : 4.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AB 180 ASN cc_start: 0.8611 (t0) cc_final: 0.8310 (t0) REVERT: 0 180 ASN cc_start: 0.8621 (t0) cc_final: 0.8315 (t0) REVERT: 4 66 MET cc_start: 0.6587 (mmt) cc_final: 0.5780 (mmt) REVERT: 4 85 THR cc_start: 0.7879 (p) cc_final: 0.7649 (t) REVERT: 4 191 GLU cc_start: 0.5877 (tm-30) cc_final: 0.5675 (tm-30) REVERT: 9 63 PRO cc_start: 0.7525 (Cg_endo) cc_final: 0.7250 (Cg_exo) REVERT: 9 66 MET cc_start: 0.7017 (mmt) cc_final: 0.6575 (mmt) REVERT: 9 191 GLU cc_start: 0.5583 (tm-30) cc_final: 0.5359 (tm-30) REVERT: A 138 LYS cc_start: 0.8253 (ptmt) cc_final: 0.8001 (tttp) REVERT: A 164 ASP cc_start: 0.7406 (p0) cc_final: 0.7120 (p0) REVERT: B 66 MET cc_start: 0.6878 (mmt) cc_final: 0.6132 (mmp) REVERT: B 188 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: C 180 ASN cc_start: 0.8595 (t0) cc_final: 0.8131 (t0) REVERT: G 63 PRO cc_start: 0.7986 (Cg_exo) cc_final: 0.7765 (Cg_endo) REVERT: K 151 ASP cc_start: 0.7059 (p0) cc_final: 0.6789 (p0) REVERT: L 117 MET cc_start: 0.7168 (ptm) cc_final: 0.6932 (ptm) REVERT: L 191 GLU cc_start: 0.5954 (tm-30) cc_final: 0.5704 (tm-30) REVERT: M 180 ASN cc_start: 0.8253 (t0) cc_final: 0.7824 (t0) REVERT: P 128 ARG cc_start: 0.8051 (tpp80) cc_final: 0.7849 (tpp80) REVERT: Q 66 MET cc_start: 0.7265 (mmt) cc_final: 0.6622 (mmp) REVERT: Q 191 GLU cc_start: 0.6002 (tm-30) cc_final: 0.5726 (tm-30) REVERT: R 180 ASN cc_start: 0.8579 (t0) cc_final: 0.8114 (t0) REVERT: U 151 ASP cc_start: 0.7191 (p0) cc_final: 0.6828 (p0) REVERT: V 66 MET cc_start: 0.6586 (mmt) cc_final: 0.6071 (mmt) REVERT: V 108 LYS cc_start: 0.7138 (tptt) cc_final: 0.6922 (tptm) REVERT: V 191 GLU cc_start: 0.6198 (tm-30) cc_final: 0.5964 (tm-30) REVERT: V 208 TRP cc_start: 0.7385 (t60) cc_final: 0.6968 (t-100) REVERT: W 187 ARG cc_start: 0.7624 (mtp85) cc_final: 0.7377 (mtm-85) REVERT: b 74 GLU cc_start: 0.7966 (mp0) cc_final: 0.7088 (mp0) REVERT: e 235 ILE cc_start: 0.8926 (mm) cc_final: 0.8699 (mm) REVERT: f 63 PRO cc_start: 0.7497 (Cg_endo) cc_final: 0.7151 (Cg_exo) REVERT: f 66 MET cc_start: 0.6667 (mmt) cc_final: 0.6162 (mmt) REVERT: j 138 LYS cc_start: 0.8270 (ptmt) cc_final: 0.8006 (tttp) REVERT: k 90 ILE cc_start: 0.8858 (mm) cc_final: 0.8580 (mm) REVERT: l 180 ASN cc_start: 0.8648 (t0) cc_final: 0.8389 (t0) REVERT: o 235 ILE cc_start: 0.9063 (mm) cc_final: 0.8815 (mm) REVERT: r 177 ASP cc_start: 0.8080 (t0) cc_final: 0.7831 (t0) REVERT: r 179 ASP cc_start: 0.7149 (p0) cc_final: 0.6838 (p0) REVERT: u 85 THR cc_start: 0.7872 (p) cc_final: 0.7597 (t) REVERT: u 191 GLU cc_start: 0.5987 (tm-30) cc_final: 0.5748 (tm-30) REVERT: v 74 GLU cc_start: 0.7608 (mp0) cc_final: 0.7250 (mp0) REVERT: x 183 GLN cc_start: 0.7685 (tt0) cc_final: 0.7242 (pt0) REVERT: x 184 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7270 (tt0) REVERT: y 66 MET cc_start: 0.7763 (mmp) cc_final: 0.7117 (mmp) REVERT: z 144 ASN cc_start: 0.8335 (t160) cc_final: 0.7651 (t0) outliers start: 159 outliers final: 117 residues processed: 1290 average time/residue: 0.4863 time to fit residues: 1063.2377 Evaluate side-chains 1302 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1183 time to evaluate : 4.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain AA residue 188 VAL Chi-restraints excluded: chain AB residue 191 VAL Chi-restraints excluded: chain 0 residue 167 ILE Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 1 residue 199 LEU Chi-restraints excluded: chain 2 residue 181 ASP Chi-restraints excluded: chain 3 residue 46 ASP Chi-restraints excluded: chain 3 residue 117 MET Chi-restraints excluded: chain 4 residue 175 THR Chi-restraints excluded: chain 5 residue 157 THR Chi-restraints excluded: chain 6 residue 179 ASP Chi-restraints excluded: chain 6 residue 188 VAL Chi-restraints excluded: chain 8 residue 216 MET Chi-restraints excluded: chain 9 residue 48 ASN Chi-restraints excluded: chain 9 residue 175 THR Chi-restraints excluded: chain 9 residue 204 GLU Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 138 LYS Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain Q residue 48 ASN Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 159 HIS Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 188 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain W residue 167 ILE Chi-restraints excluded: chain X residue 179 ASP Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Z residue 220 ASN Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 223 THR Chi-restraints excluded: chain b residue 188 VAL Chi-restraints excluded: chain d residue 181 ASP Chi-restraints excluded: chain e residue 117 MET Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 188 ASP Chi-restraints excluded: chain e residue 216 MET Chi-restraints excluded: chain f residue 48 ASN Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 174 VAL Chi-restraints excluded: chain g residue 157 THR Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain h residue 179 ASP Chi-restraints excluded: chain j residue 46 ASP Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain j residue 92 VAL Chi-restraints excluded: chain j residue 188 ASP Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 173 SER Chi-restraints excluded: chain k residue 188 ASP Chi-restraints excluded: chain l residue 157 THR Chi-restraints excluded: chain m residue 179 ASP Chi-restraints excluded: chain m residue 196 ASP Chi-restraints excluded: chain n residue 181 ASP Chi-restraints excluded: chain o residue 134 GLN Chi-restraints excluded: chain o residue 141 ILE Chi-restraints excluded: chain o residue 224 LEU Chi-restraints excluded: chain p residue 48 ASN Chi-restraints excluded: chain p residue 162 LEU Chi-restraints excluded: chain p residue 173 SER Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain q residue 191 VAL Chi-restraints excluded: chain t residue 46 ASP Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 141 ILE Chi-restraints excluded: chain u residue 147 VAL Chi-restraints excluded: chain u residue 162 LEU Chi-restraints excluded: chain u residue 175 THR Chi-restraints excluded: chain v residue 73 VAL Chi-restraints excluded: chain v residue 157 THR Chi-restraints excluded: chain w residue 179 ASP Chi-restraints excluded: chain x residue 184 GLU Chi-restraints excluded: chain y residue 46 ASP Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 143 LEU Chi-restraints excluded: chain y residue 224 LEU Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 116 LEU Chi-restraints excluded: chain z residue 175 THR Chi-restraints excluded: chain z residue 204 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 689 random chunks: chunk 619 optimal weight: 0.0270 chunk 471 optimal weight: 0.8980 chunk 325 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 299 optimal weight: 6.9990 chunk 420 optimal weight: 10.0000 chunk 629 optimal weight: 1.9990 chunk 665 optimal weight: 1.9990 chunk 328 optimal weight: 5.9990 chunk 596 optimal weight: 0.7980 chunk 179 optimal weight: 0.0270 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 166 GLN 9 48 ASN ** 9 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS F 222 GLN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 ASN L 184 GLN ** Q 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 159 HIS U 222 GLN ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 184 GLN ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 184 GLN t 222 GLN ** u 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 37 GLN z 48 ASN ** z 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 55744 Z= 0.175 Angle : 0.600 10.254 75907 Z= 0.298 Chirality : 0.043 0.210 8515 Planarity : 0.006 0.074 9919 Dihedral : 4.655 57.366 7715 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 3.74 % Allowed : 18.61 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.10), residues: 6968 helix: -1.23 (0.19), residues: 624 sheet: -1.82 (0.11), residues: 2236 loop : -2.38 (0.09), residues: 4108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 4 208 HIS 0.003 0.001 HIS r 159 PHE 0.012 0.001 PHE U 38 TYR 0.012 0.001 TYR 4 190 ARG 0.005 0.000 ARG U 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1424 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1208 time to evaluate : 4.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 180 ASN cc_start: 0.8621 (t0) cc_final: 0.8312 (t0) REVERT: 0 180 ASN cc_start: 0.8630 (t0) cc_final: 0.8377 (t0) REVERT: 9 66 MET cc_start: 0.7005 (mmt) cc_final: 0.6561 (mmt) REVERT: 9 191 GLU cc_start: 0.5504 (tm-30) cc_final: 0.5255 (tm-30) REVERT: A 129 LYS cc_start: 0.8834 (ptpp) cc_final: 0.8623 (ptpp) REVERT: A 138 LYS cc_start: 0.8205 (ptmt) cc_final: 0.7889 (tttp) REVERT: A 164 ASP cc_start: 0.7654 (p0) cc_final: 0.7394 (p0) REVERT: B 66 MET cc_start: 0.6917 (mmt) cc_final: 0.6551 (mmt) REVERT: B 188 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7166 (m-30) REVERT: C 180 ASN cc_start: 0.8582 (t0) cc_final: 0.8107 (t0) REVERT: G 49 MET cc_start: 0.7400 (ttt) cc_final: 0.7121 (ttt) REVERT: G 66 MET cc_start: 0.6814 (mmp) cc_final: 0.6081 (mmp) REVERT: G 67 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6494 (pp) REVERT: G 144 ASN cc_start: 0.8406 (t0) cc_final: 0.8193 (t0) REVERT: G 216 MET cc_start: 0.7564 (ttp) cc_final: 0.7319 (ttp) REVERT: K 129 LYS cc_start: 0.8740 (ptpp) cc_final: 0.8402 (ptpp) REVERT: K 151 ASP cc_start: 0.7052 (p0) cc_final: 0.6774 (p0) REVERT: L 117 MET cc_start: 0.7177 (ptm) cc_final: 0.6960 (ptm) REVERT: M 180 ASN cc_start: 0.8272 (t0) cc_final: 0.7838 (t0) REVERT: Q 66 MET cc_start: 0.7283 (mmt) cc_final: 0.6664 (mmp) REVERT: Q 191 GLU cc_start: 0.5849 (tm-30) cc_final: 0.5604 (tm-30) REVERT: R 180 ASN cc_start: 0.8594 (t0) cc_final: 0.8187 (t0) REVERT: V 66 MET cc_start: 0.6611 (mmt) cc_final: 0.6249 (mmt) REVERT: V 108 LYS cc_start: 0.7164 (tptt) cc_final: 0.6943 (tptm) REVERT: V 208 TRP cc_start: 0.7303 (t60) cc_final: 0.6970 (t-100) REVERT: W 187 ARG cc_start: 0.7652 (mtp85) cc_final: 0.7447 (mtm-85) REVERT: X 177 ASP cc_start: 0.8024 (t0) cc_final: 0.7804 (t0) REVERT: b 74 GLU cc_start: 0.7908 (mp0) cc_final: 0.7101 (mp0) REVERT: e 235 ILE cc_start: 0.8963 (mm) cc_final: 0.8720 (mm) REVERT: f 66 MET cc_start: 0.6688 (mmt) cc_final: 0.6127 (mmt) REVERT: j 138 LYS cc_start: 0.8234 (ptmt) cc_final: 0.7966 (tttp) REVERT: j 164 ASP cc_start: 0.7551 (p0) cc_final: 0.7332 (p0) REVERT: k 85 THR cc_start: 0.7834 (OUTLIER) cc_final: 0.7604 (t) REVERT: k 90 ILE cc_start: 0.8818 (mm) cc_final: 0.8546 (mm) REVERT: l 180 ASN cc_start: 0.8600 (t0) cc_final: 0.8305 (t0) REVERT: o 235 ILE cc_start: 0.9046 (mm) cc_final: 0.8809 (mm) REVERT: r 177 ASP cc_start: 0.8147 (t0) cc_final: 0.7897 (t70) REVERT: r 179 ASP cc_start: 0.7114 (p0) cc_final: 0.6694 (p0) REVERT: t 138 LYS cc_start: 0.8122 (ptmt) cc_final: 0.7918 (tttp) REVERT: u 85 THR cc_start: 0.7780 (OUTLIER) cc_final: 0.7486 (t) REVERT: v 74 GLU cc_start: 0.7539 (mp0) cc_final: 0.7239 (mp0) REVERT: x 184 GLU cc_start: 0.7536 (tt0) cc_final: 0.7265 (tt0) REVERT: y 66 MET cc_start: 0.7643 (mmp) cc_final: 0.6974 (mmp) outliers start: 216 outliers final: 153 residues processed: 1319 average time/residue: 0.4824 time to fit residues: 1088.9814 Evaluate side-chains 1328 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1171 time to evaluate : 4.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain AA residue 188 VAL Chi-restraints excluded: chain AB residue 188 VAL Chi-restraints excluded: chain AB residue 191 VAL Chi-restraints excluded: chain AC residue 181 ASP Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 2 residue 181 ASP Chi-restraints excluded: chain 3 residue 46 ASP Chi-restraints excluded: chain 3 residue 117 MET Chi-restraints excluded: chain 3 residue 188 ASP Chi-restraints excluded: chain 4 residue 127 THR Chi-restraints excluded: chain 4 residue 175 THR Chi-restraints excluded: chain 4 residue 206 ASP Chi-restraints excluded: chain 4 residue 230 MET Chi-restraints excluded: chain 5 residue 157 THR Chi-restraints excluded: chain 6 residue 179 ASP Chi-restraints excluded: chain 8 residue 46 ASP Chi-restraints excluded: chain 8 residue 116 LEU Chi-restraints excluded: chain 8 residue 143 LEU Chi-restraints excluded: chain 8 residue 216 MET Chi-restraints excluded: chain 9 residue 48 ASN Chi-restraints excluded: chain 9 residue 127 THR Chi-restraints excluded: chain 9 residue 175 THR Chi-restraints excluded: chain 9 residue 204 GLU Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 138 LYS Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 184 GLN Chi-restraints excluded: chain L residue 206 ASP Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain Q residue 48 ASN Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 159 HIS Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 188 VAL Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain V residue 26 SER Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain W residue 167 ILE Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain X residue 179 ASP Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Z residue 117 MET Chi-restraints excluded: chain Z residue 216 MET Chi-restraints excluded: chain Z residue 220 ASN Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 127 THR Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 223 THR Chi-restraints excluded: chain b residue 188 VAL Chi-restraints excluded: chain d residue 181 ASP Chi-restraints excluded: chain e residue 117 MET Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 188 ASP Chi-restraints excluded: chain e residue 216 MET Chi-restraints excluded: chain e residue 224 LEU Chi-restraints excluded: chain f residue 48 ASN Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 174 VAL Chi-restraints excluded: chain f residue 175 THR Chi-restraints excluded: chain f residue 204 GLU Chi-restraints excluded: chain g residue 157 THR Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain h residue 179 ASP Chi-restraints excluded: chain j residue 46 ASP Chi-restraints excluded: chain j residue 117 MET Chi-restraints excluded: chain j residue 188 ASP Chi-restraints excluded: chain j residue 216 MET Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 127 THR Chi-restraints excluded: chain k residue 173 SER Chi-restraints excluded: chain k residue 206 ASP Chi-restraints excluded: chain l residue 157 THR Chi-restraints excluded: chain l residue 188 VAL Chi-restraints excluded: chain m residue 179 ASP Chi-restraints excluded: chain n residue 181 ASP Chi-restraints excluded: chain o residue 188 ASP Chi-restraints excluded: chain o residue 224 LEU Chi-restraints excluded: chain p residue 48 ASN Chi-restraints excluded: chain p residue 49 MET Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 173 SER Chi-restraints excluded: chain p residue 175 THR Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain q residue 191 VAL Chi-restraints excluded: chain t residue 46 ASP Chi-restraints excluded: chain t residue 48 ASN Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 141 ILE Chi-restraints excluded: chain t residue 216 MET Chi-restraints excluded: chain t residue 224 LEU Chi-restraints excluded: chain u residue 85 THR Chi-restraints excluded: chain u residue 127 THR Chi-restraints excluded: chain u residue 175 THR Chi-restraints excluded: chain u residue 206 ASP Chi-restraints excluded: chain v residue 73 VAL Chi-restraints excluded: chain v residue 157 THR Chi-restraints excluded: chain w residue 179 ASP Chi-restraints excluded: chain y residue 46 ASP Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 143 LEU Chi-restraints excluded: chain y residue 188 ASP Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 175 THR Chi-restraints excluded: chain z residue 204 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 689 random chunks: chunk 554 optimal weight: 6.9990 chunk 378 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 495 optimal weight: 7.9990 chunk 274 optimal weight: 3.9990 chunk 568 optimal weight: 1.9990 chunk 460 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 340 optimal weight: 0.8980 chunk 597 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 48 ASN 9 184 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 ASN L 184 GLN ** Q 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 159 HIS U 222 GLN ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 48 ASN ** V 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 222 GLN ** k 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 134 GLN ** u 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 48 ASN ** u 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 48 ASN ** z 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 55744 Z= 0.264 Angle : 0.623 10.074 75907 Z= 0.312 Chirality : 0.043 0.193 8515 Planarity : 0.006 0.076 9919 Dihedral : 4.654 51.445 7714 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.05 % Favored : 86.95 % Rotamer: Outliers : 4.66 % Allowed : 19.65 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.10), residues: 6968 helix: -1.13 (0.19), residues: 624 sheet: -1.83 (0.11), residues: 2340 loop : -2.39 (0.10), residues: 4004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 208 HIS 0.003 0.001 HIS v 183 PHE 0.012 0.001 PHE q 190 TYR 0.017 0.002 TYR L 136 ARG 0.006 0.000 ARG P 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1469 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1200 time to evaluate : 4.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AB 180 ASN cc_start: 0.8613 (t0) cc_final: 0.8300 (t0) REVERT: 3 85 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7805 (m) REVERT: 4 56 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7793 (tptt) REVERT: 4 66 MET cc_start: 0.6988 (mmt) cc_final: 0.5907 (mmt) REVERT: 9 63 PRO cc_start: 0.7537 (Cg_endo) cc_final: 0.7317 (Cg_exo) REVERT: 9 66 MET cc_start: 0.7068 (mmt) cc_final: 0.6565 (mmt) REVERT: 9 191 GLU cc_start: 0.5468 (tm-30) cc_final: 0.5154 (tm-30) REVERT: A 129 LYS cc_start: 0.8779 (ptpp) cc_final: 0.8465 (ptpp) REVERT: A 138 LYS cc_start: 0.8273 (ptmt) cc_final: 0.7983 (tttp) REVERT: A 164 ASP cc_start: 0.7578 (p0) cc_final: 0.7297 (p0) REVERT: B 66 MET cc_start: 0.6792 (mmt) cc_final: 0.6400 (mmt) REVERT: B 188 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7136 (m-30) REVERT: C 180 ASN cc_start: 0.8646 (t0) cc_final: 0.8261 (t0) REVERT: F 129 LYS cc_start: 0.8804 (ptpp) cc_final: 0.8420 (ptpp) REVERT: G 49 MET cc_start: 0.7536 (ttt) cc_final: 0.7239 (ttt) REVERT: G 66 MET cc_start: 0.6974 (mmt) cc_final: 0.6314 (mmp) REVERT: G 216 MET cc_start: 0.7615 (ttp) cc_final: 0.7387 (ttp) REVERT: H 74 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: K 151 ASP cc_start: 0.7090 (p0) cc_final: 0.6785 (p0) REVERT: L 117 MET cc_start: 0.7210 (ptm) cc_final: 0.6955 (ptm) REVERT: L 208 TRP cc_start: 0.7208 (t60) cc_final: 0.6900 (t-100) REVERT: M 180 ASN cc_start: 0.8312 (t0) cc_final: 0.7922 (t0) REVERT: P 128 ARG cc_start: 0.8036 (tpp80) cc_final: 0.7833 (tpp80) REVERT: Q 66 MET cc_start: 0.7190 (mmt) cc_final: 0.6508 (mmp) REVERT: Q 191 GLU cc_start: 0.5846 (tm-30) cc_final: 0.5586 (tm-30) REVERT: R 180 ASN cc_start: 0.8593 (t0) cc_final: 0.8255 (t0) REVERT: V 108 LYS cc_start: 0.7372 (tptt) cc_final: 0.7145 (tptm) REVERT: V 208 TRP cc_start: 0.7307 (t60) cc_final: 0.6914 (t-100) REVERT: W 74 GLU cc_start: 0.8226 (mp0) cc_final: 0.7721 (mp0) REVERT: X 177 ASP cc_start: 0.8023 (t0) cc_final: 0.7800 (t0) REVERT: Z 66 MET cc_start: 0.7508 (mmm) cc_final: 0.7191 (mmm) REVERT: Z 138 LYS cc_start: 0.8201 (ptmt) cc_final: 0.7932 (tttp) REVERT: b 74 GLU cc_start: 0.8041 (mp0) cc_final: 0.7252 (mp0) REVERT: b 157 THR cc_start: 0.6367 (OUTLIER) cc_final: 0.5953 (p) REVERT: e 235 ILE cc_start: 0.9019 (mm) cc_final: 0.8738 (mm) REVERT: f 63 PRO cc_start: 0.7338 (Cg_endo) cc_final: 0.7071 (Cg_exo) REVERT: f 66 MET cc_start: 0.6719 (mmt) cc_final: 0.5575 (mmp) REVERT: j 129 LYS cc_start: 0.8702 (ptpp) cc_final: 0.8317 (ptpp) REVERT: j 138 LYS cc_start: 0.8254 (ptmt) cc_final: 0.8016 (tttp) REVERT: j 164 ASP cc_start: 0.7818 (p0) cc_final: 0.7524 (p0) REVERT: k 90 ILE cc_start: 0.8979 (mm) cc_final: 0.8729 (mm) REVERT: k 144 ASN cc_start: 0.8580 (t0) cc_final: 0.8322 (t0) REVERT: l 180 ASN cc_start: 0.8606 (t0) cc_final: 0.8322 (t0) REVERT: o 235 ILE cc_start: 0.9051 (mm) cc_final: 0.8788 (mm) REVERT: r 177 ASP cc_start: 0.8107 (t0) cc_final: 0.7841 (t70) REVERT: r 179 ASP cc_start: 0.7178 (p0) cc_final: 0.6703 (p0) REVERT: t 184 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: u 85 THR cc_start: 0.7772 (OUTLIER) cc_final: 0.7500 (t) REVERT: v 74 GLU cc_start: 0.7595 (mp0) cc_final: 0.7301 (mp0) REVERT: v 196 ASP cc_start: 0.8102 (p0) cc_final: 0.7880 (p0) REVERT: z 144 ASN cc_start: 0.8577 (t0) cc_final: 0.8060 (t0) outliers start: 269 outliers final: 205 residues processed: 1340 average time/residue: 0.4756 time to fit residues: 1087.7578 Evaluate side-chains 1390 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1178 time to evaluate : 4.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain AA residue 188 VAL Chi-restraints excluded: chain AA residue 196 ASP Chi-restraints excluded: chain AB residue 188 VAL Chi-restraints excluded: chain AB residue 191 VAL Chi-restraints excluded: chain AC residue 181 ASP Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 2 residue 181 ASP Chi-restraints excluded: chain 2 residue 184 GLU Chi-restraints excluded: chain 3 residue 46 ASP Chi-restraints excluded: chain 3 residue 48 ASN Chi-restraints excluded: chain 3 residue 85 THR Chi-restraints excluded: chain 3 residue 117 MET Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 3 residue 188 ASP Chi-restraints excluded: chain 3 residue 216 MET Chi-restraints excluded: chain 4 residue 56 LYS Chi-restraints excluded: chain 4 residue 85 THR Chi-restraints excluded: chain 4 residue 127 THR Chi-restraints excluded: chain 4 residue 162 LEU Chi-restraints excluded: chain 4 residue 175 THR Chi-restraints excluded: chain 4 residue 206 ASP Chi-restraints excluded: chain 4 residue 230 MET Chi-restraints excluded: chain 5 residue 192 VAL Chi-restraints excluded: chain 6 residue 179 ASP Chi-restraints excluded: chain 6 residue 180 ASN Chi-restraints excluded: chain 6 residue 188 VAL Chi-restraints excluded: chain 7 residue 181 ASP Chi-restraints excluded: chain 8 residue 46 ASP Chi-restraints excluded: chain 8 residue 116 LEU Chi-restraints excluded: chain 8 residue 168 LEU Chi-restraints excluded: chain 8 residue 192 LEU Chi-restraints excluded: chain 8 residue 216 MET Chi-restraints excluded: chain 9 residue 127 THR Chi-restraints excluded: chain 9 residue 175 THR Chi-restraints excluded: chain 9 residue 204 GLU Chi-restraints excluded: chain 9 residue 206 ASP Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 138 LYS Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 206 ASP Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 216 MET Chi-restraints excluded: chain Q residue 48 ASN Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain Q residue 206 ASP Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 159 HIS Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 188 VAL Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 48 ASN Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 168 LEU Chi-restraints excluded: chain U residue 224 LEU Chi-restraints excluded: chain V residue 85 THR Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 147 VAL Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 ASP Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain W residue 167 ILE Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain X residue 179 ASP Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Z residue 117 MET Chi-restraints excluded: chain Z residue 145 ARG Chi-restraints excluded: chain Z residue 168 LEU Chi-restraints excluded: chain Z residue 188 ASP Chi-restraints excluded: chain Z residue 216 MET Chi-restraints excluded: chain Z residue 220 ASN Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain a residue 127 THR Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 223 THR Chi-restraints excluded: chain b residue 157 THR Chi-restraints excluded: chain b residue 188 VAL Chi-restraints excluded: chain d residue 181 ASP Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 117 MET Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain e residue 188 ASP Chi-restraints excluded: chain e residue 216 MET Chi-restraints excluded: chain f residue 48 ASN Chi-restraints excluded: chain f residue 85 THR Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 174 VAL Chi-restraints excluded: chain f residue 175 THR Chi-restraints excluded: chain f residue 204 GLU Chi-restraints excluded: chain f residue 206 ASP Chi-restraints excluded: chain g residue 157 THR Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain h residue 179 ASP Chi-restraints excluded: chain j residue 46 ASP Chi-restraints excluded: chain j residue 48 ASN Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain j residue 117 MET Chi-restraints excluded: chain j residue 168 LEU Chi-restraints excluded: chain j residue 188 ASP Chi-restraints excluded: chain j residue 216 MET Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 127 THR Chi-restraints excluded: chain k residue 173 SER Chi-restraints excluded: chain k residue 188 ASP Chi-restraints excluded: chain k residue 206 ASP Chi-restraints excluded: chain l residue 157 THR Chi-restraints excluded: chain l residue 188 VAL Chi-restraints excluded: chain l residue 203 VAL Chi-restraints excluded: chain m residue 179 ASP Chi-restraints excluded: chain m residue 196 ASP Chi-restraints excluded: chain n residue 181 ASP Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 163 SER Chi-restraints excluded: chain o residue 168 LEU Chi-restraints excluded: chain o residue 188 ASP Chi-restraints excluded: chain o residue 224 LEU Chi-restraints excluded: chain p residue 48 ASN Chi-restraints excluded: chain p residue 49 MET Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 173 SER Chi-restraints excluded: chain p residue 175 THR Chi-restraints excluded: chain p residue 206 ASP Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain q residue 191 VAL Chi-restraints excluded: chain t residue 46 ASP Chi-restraints excluded: chain t residue 48 ASN Chi-restraints excluded: chain t residue 81 THR Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 141 ILE Chi-restraints excluded: chain t residue 168 LEU Chi-restraints excluded: chain t residue 184 GLN Chi-restraints excluded: chain t residue 216 MET Chi-restraints excluded: chain t residue 224 LEU Chi-restraints excluded: chain u residue 85 THR Chi-restraints excluded: chain u residue 127 THR Chi-restraints excluded: chain u residue 162 LEU Chi-restraints excluded: chain u residue 175 THR Chi-restraints excluded: chain u residue 206 ASP Chi-restraints excluded: chain v residue 73 VAL Chi-restraints excluded: chain v residue 157 THR Chi-restraints excluded: chain w residue 179 ASP Chi-restraints excluded: chain y residue 32 LEU Chi-restraints excluded: chain y residue 46 ASP Chi-restraints excluded: chain y residue 117 MET Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 143 LEU Chi-restraints excluded: chain y residue 168 LEU Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 175 THR Chi-restraints excluded: chain z residue 204 GLU Chi-restraints excluded: chain z residue 206 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 689 random chunks: chunk 224 optimal weight: 4.9990 chunk 599 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 391 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 666 optimal weight: 1.9990 chunk 553 optimal weight: 7.9990 chunk 308 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 220 optimal weight: 5.9990 chunk 349 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 134 GLN 9 184 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN G 184 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 GLN P 205 GLN ** Q 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 238 ASN f 144 ASN ** f 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 222 GLN ** k 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 48 ASN k 144 ASN ** k 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 134 GLN ** u 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 37 GLN ** u 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 134 GLN z 48 ASN ** z 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 55744 Z= 0.282 Angle : 0.633 10.204 75907 Z= 0.318 Chirality : 0.044 0.331 8515 Planarity : 0.006 0.081 9919 Dihedral : 4.704 46.001 7714 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.69 % Favored : 87.31 % Rotamer: Outliers : 5.21 % Allowed : 20.39 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.10), residues: 6968 helix: -1.09 (0.19), residues: 624 sheet: -1.74 (0.10), residues: 2522 loop : -2.62 (0.10), residues: 3822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 208 HIS 0.003 0.001 HIS v 183 PHE 0.011 0.002 PHE 3 51 TYR 0.019 0.002 TYR 4 136 ARG 0.007 0.000 ARG k 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1498 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 1197 time to evaluate : 4.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 180 ASN cc_start: 0.8614 (t0) cc_final: 0.8272 (t0) REVERT: 3 85 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7767 (m) REVERT: 4 56 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7663 (tptt) REVERT: 4 66 MET cc_start: 0.6844 (mmt) cc_final: 0.5953 (mmt) REVERT: 9 63 PRO cc_start: 0.7517 (Cg_endo) cc_final: 0.7299 (Cg_exo) REVERT: 9 66 MET cc_start: 0.7004 (mmt) cc_final: 0.6530 (mmt) REVERT: 9 191 GLU cc_start: 0.5456 (tm-30) cc_final: 0.5254 (tm-30) REVERT: A 138 LYS cc_start: 0.8248 (ptmt) cc_final: 0.7963 (tttp) REVERT: B 66 MET cc_start: 0.6755 (mmt) cc_final: 0.6421 (mmt) REVERT: B 188 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.7116 (m-30) REVERT: C 180 ASN cc_start: 0.8695 (t0) cc_final: 0.8340 (t0) REVERT: G 49 MET cc_start: 0.7578 (ttt) cc_final: 0.7267 (ttt) REVERT: G 216 MET cc_start: 0.7606 (ttp) cc_final: 0.7390 (ttp) REVERT: L 117 MET cc_start: 0.7139 (ptm) cc_final: 0.6857 (ptm) REVERT: M 180 ASN cc_start: 0.8430 (t0) cc_final: 0.8033 (t0) REVERT: P 128 ARG cc_start: 0.8010 (tpp80) cc_final: 0.7807 (tpp80) REVERT: P 205 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7726 (mp10) REVERT: Q 66 MET cc_start: 0.7213 (mmt) cc_final: 0.6520 (mmp) REVERT: Q 110 GLU cc_start: 0.6620 (tp30) cc_final: 0.6094 (tm-30) REVERT: Q 191 GLU cc_start: 0.6042 (tm-30) cc_final: 0.5752 (tm-30) REVERT: R 180 ASN cc_start: 0.8603 (t0) cc_final: 0.8291 (t0) REVERT: V 108 LYS cc_start: 0.7386 (tptt) cc_final: 0.7181 (tptm) REVERT: V 208 TRP cc_start: 0.7311 (t60) cc_final: 0.6878 (t-100) REVERT: W 74 GLU cc_start: 0.8242 (mp0) cc_final: 0.7729 (mp0) REVERT: X 199 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7881 (mm) REVERT: Z 138 LYS cc_start: 0.8205 (ptmt) cc_final: 0.7936 (tttp) REVERT: b 157 THR cc_start: 0.6257 (OUTLIER) cc_final: 0.6045 (m) REVERT: e 235 ILE cc_start: 0.9004 (mm) cc_final: 0.8736 (mm) REVERT: f 63 PRO cc_start: 0.7375 (Cg_endo) cc_final: 0.7112 (Cg_exo) REVERT: f 66 MET cc_start: 0.6686 (mmt) cc_final: 0.6160 (mmt) REVERT: h 198 VAL cc_start: 0.7975 (OUTLIER) cc_final: 0.7769 (p) REVERT: j 129 LYS cc_start: 0.8752 (ptpp) cc_final: 0.8362 (ptpp) REVERT: j 138 LYS cc_start: 0.8263 (ptmt) cc_final: 0.8034 (tttp) REVERT: j 164 ASP cc_start: 0.7672 (p0) cc_final: 0.7389 (p0) REVERT: k 90 ILE cc_start: 0.9017 (mm) cc_final: 0.8776 (mm) REVERT: k 216 MET cc_start: 0.7299 (mtt) cc_final: 0.7068 (mtp) REVERT: l 180 ASN cc_start: 0.8555 (t0) cc_final: 0.8275 (t0) REVERT: o 128 ARG cc_start: 0.8260 (tpp80) cc_final: 0.7995 (tpp80) REVERT: o 235 ILE cc_start: 0.9034 (mm) cc_final: 0.8777 (mm) REVERT: r 177 ASP cc_start: 0.8119 (t0) cc_final: 0.7833 (t70) REVERT: r 179 ASP cc_start: 0.7176 (p0) cc_final: 0.6668 (p0) REVERT: t 184 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: v 74 GLU cc_start: 0.7642 (mp0) cc_final: 0.7423 (mp0) REVERT: v 196 ASP cc_start: 0.8133 (p0) cc_final: 0.7928 (p0) outliers start: 301 outliers final: 234 residues processed: 1372 average time/residue: 0.4782 time to fit residues: 1117.4796 Evaluate side-chains 1424 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1182 time to evaluate : 5.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain AA residue 188 VAL Chi-restraints excluded: chain AB residue 188 VAL Chi-restraints excluded: chain AB residue 191 VAL Chi-restraints excluded: chain AC residue 181 ASP Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 2 residue 181 ASP Chi-restraints excluded: chain 2 residue 184 GLU Chi-restraints excluded: chain 3 residue 40 LEU Chi-restraints excluded: chain 3 residue 46 ASP Chi-restraints excluded: chain 3 residue 48 ASN Chi-restraints excluded: chain 3 residue 85 THR Chi-restraints excluded: chain 3 residue 117 MET Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 3 residue 216 MET Chi-restraints excluded: chain 4 residue 56 LYS Chi-restraints excluded: chain 4 residue 85 THR Chi-restraints excluded: chain 4 residue 127 THR Chi-restraints excluded: chain 4 residue 147 VAL Chi-restraints excluded: chain 4 residue 162 LEU Chi-restraints excluded: chain 4 residue 175 THR Chi-restraints excluded: chain 4 residue 206 ASP Chi-restraints excluded: chain 4 residue 230 MET Chi-restraints excluded: chain 5 residue 157 THR Chi-restraints excluded: chain 5 residue 192 VAL Chi-restraints excluded: chain 6 residue 180 ASN Chi-restraints excluded: chain 6 residue 188 VAL Chi-restraints excluded: chain 7 residue 181 ASP Chi-restraints excluded: chain 8 residue 44 ASN Chi-restraints excluded: chain 8 residue 46 ASP Chi-restraints excluded: chain 8 residue 81 THR Chi-restraints excluded: chain 8 residue 141 ILE Chi-restraints excluded: chain 8 residue 143 LEU Chi-restraints excluded: chain 8 residue 163 SER Chi-restraints excluded: chain 8 residue 168 LEU Chi-restraints excluded: chain 8 residue 192 LEU Chi-restraints excluded: chain 8 residue 216 MET Chi-restraints excluded: chain 9 residue 48 ASN Chi-restraints excluded: chain 9 residue 127 THR Chi-restraints excluded: chain 9 residue 175 THR Chi-restraints excluded: chain 9 residue 204 GLU Chi-restraints excluded: chain 9 residue 206 ASP Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain K residue 44 ASN Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 184 GLN Chi-restraints excluded: chain L residue 206 ASP Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain N residue 159 HIS Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain P residue 44 ASN Chi-restraints excluded: chain P residue 48 ASN Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 163 SER Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 216 MET Chi-restraints excluded: chain Q residue 48 ASN Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain Q residue 206 ASP Chi-restraints excluded: chain Q residue 225 MET Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 159 HIS Chi-restraints excluded: chain S residue 188 VAL Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 48 ASN Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 168 LEU Chi-restraints excluded: chain U residue 224 LEU Chi-restraints excluded: chain V residue 85 THR Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 147 VAL Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 ASP Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain W residue 167 ILE Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain X residue 179 ASP Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Z residue 44 ASN Chi-restraints excluded: chain Z residue 60 ILE Chi-restraints excluded: chain Z residue 117 MET Chi-restraints excluded: chain Z residue 145 ARG Chi-restraints excluded: chain Z residue 168 LEU Chi-restraints excluded: chain Z residue 188 ASP Chi-restraints excluded: chain Z residue 216 MET Chi-restraints excluded: chain Z residue 220 ASN Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain a residue 127 THR Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 206 ASP Chi-restraints excluded: chain a residue 223 THR Chi-restraints excluded: chain b residue 157 THR Chi-restraints excluded: chain b residue 188 VAL Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain d residue 181 ASP Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 117 MET Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain e residue 188 ASP Chi-restraints excluded: chain e residue 216 MET Chi-restraints excluded: chain f residue 48 ASN Chi-restraints excluded: chain f residue 85 THR Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 175 THR Chi-restraints excluded: chain f residue 204 GLU Chi-restraints excluded: chain g residue 157 THR Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain h residue 179 ASP Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain j residue 46 ASP Chi-restraints excluded: chain j residue 48 ASN Chi-restraints excluded: chain j residue 117 MET Chi-restraints excluded: chain j residue 163 SER Chi-restraints excluded: chain j residue 168 LEU Chi-restraints excluded: chain j residue 188 ASP Chi-restraints excluded: chain j residue 216 MET Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 127 THR Chi-restraints excluded: chain k residue 173 SER Chi-restraints excluded: chain k residue 188 ASP Chi-restraints excluded: chain k residue 206 ASP Chi-restraints excluded: chain l residue 157 THR Chi-restraints excluded: chain l residue 188 VAL Chi-restraints excluded: chain m residue 179 ASP Chi-restraints excluded: chain m residue 196 ASP Chi-restraints excluded: chain n residue 181 ASP Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 44 ASN Chi-restraints excluded: chain o residue 163 SER Chi-restraints excluded: chain o residue 168 LEU Chi-restraints excluded: chain o residue 188 ASP Chi-restraints excluded: chain p residue 48 ASN Chi-restraints excluded: chain p residue 49 MET Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 173 SER Chi-restraints excluded: chain p residue 175 THR Chi-restraints excluded: chain p residue 206 ASP Chi-restraints excluded: chain q residue 73 VAL Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain q residue 191 VAL Chi-restraints excluded: chain t residue 46 ASP Chi-restraints excluded: chain t residue 48 ASN Chi-restraints excluded: chain t residue 81 THR Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 141 ILE Chi-restraints excluded: chain t residue 168 LEU Chi-restraints excluded: chain t residue 184 GLN Chi-restraints excluded: chain t residue 216 MET Chi-restraints excluded: chain t residue 224 LEU Chi-restraints excluded: chain u residue 85 THR Chi-restraints excluded: chain u residue 127 THR Chi-restraints excluded: chain u residue 162 LEU Chi-restraints excluded: chain u residue 175 THR Chi-restraints excluded: chain u residue 206 ASP Chi-restraints excluded: chain v residue 73 VAL Chi-restraints excluded: chain v residue 157 THR Chi-restraints excluded: chain w residue 179 ASP Chi-restraints excluded: chain y residue 40 LEU Chi-restraints excluded: chain y residue 44 ASN Chi-restraints excluded: chain y residue 46 ASP Chi-restraints excluded: chain y residue 117 MET Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 143 LEU Chi-restraints excluded: chain y residue 168 LEU Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 50 ILE Chi-restraints excluded: chain z residue 175 THR Chi-restraints excluded: chain z residue 204 GLU Chi-restraints excluded: chain z residue 206 ASP Chi-restraints excluded: chain z residue 216 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 689 random chunks: chunk 642 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 379 optimal weight: 1.9990 chunk 486 optimal weight: 0.9990 chunk 377 optimal weight: 3.9990 chunk 561 optimal weight: 0.0370 chunk 372 optimal weight: 5.9990 chunk 664 optimal weight: 0.0870 chunk 415 optimal weight: 7.9990 chunk 404 optimal weight: 0.8980 chunk 306 optimal weight: 2.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 222 GLN ** 4 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 184 GLN 7 183 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 GLN ** Q 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 222 GLN ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 48 ASN f 144 ASN ** f 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 144 ASN ** k 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 180 ASN ** u 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 134 GLN z 48 ASN ** z 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 55744 Z= 0.185 Angle : 0.617 11.473 75907 Z= 0.305 Chirality : 0.043 0.328 8515 Planarity : 0.006 0.076 9919 Dihedral : 4.445 47.051 7710 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 4.61 % Allowed : 21.47 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.10), residues: 6968 helix: -0.89 (0.19), residues: 624 sheet: -1.60 (0.10), residues: 2522 loop : -2.50 (0.10), residues: 3822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 208 HIS 0.002 0.001 HIS b 183 PHE 0.014 0.001 PHE K 38 TYR 0.010 0.001 TYR 4 190 ARG 0.011 0.000 ARG j 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1457 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1191 time to evaluate : 4.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 180 ASN cc_start: 0.8608 (t0) cc_final: 0.8281 (t0) REVERT: 3 85 THR cc_start: 0.7911 (OUTLIER) cc_final: 0.7672 (m) REVERT: 4 56 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7698 (tptt) REVERT: 4 166 ILE cc_start: 0.7504 (pt) cc_final: 0.7279 (mm) REVERT: 9 66 MET cc_start: 0.7105 (mmt) cc_final: 0.6722 (mmt) REVERT: 9 159 VAL cc_start: 0.8836 (m) cc_final: 0.8634 (m) REVERT: A 129 LYS cc_start: 0.8806 (ptpp) cc_final: 0.8522 (ptpp) REVERT: A 138 LYS cc_start: 0.8201 (ptmt) cc_final: 0.7914 (tttp) REVERT: B 66 MET cc_start: 0.6903 (mmt) cc_final: 0.6618 (mmt) REVERT: B 188 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6993 (m-30) REVERT: C 180 ASN cc_start: 0.8635 (t0) cc_final: 0.8344 (t0) REVERT: G 49 MET cc_start: 0.7493 (ttt) cc_final: 0.7133 (ttt) REVERT: L 117 MET cc_start: 0.7110 (ptm) cc_final: 0.6861 (ptm) REVERT: L 208 TRP cc_start: 0.7141 (t60) cc_final: 0.6858 (t-100) REVERT: M 180 ASN cc_start: 0.8462 (t0) cc_final: 0.8075 (t0) REVERT: Q 191 GLU cc_start: 0.5960 (tm-30) cc_final: 0.5693 (tm-30) REVERT: V 108 LYS cc_start: 0.7372 (tptt) cc_final: 0.7161 (tptm) REVERT: V 208 TRP cc_start: 0.7294 (t60) cc_final: 0.6958 (t-100) REVERT: W 74 GLU cc_start: 0.8119 (mp0) cc_final: 0.7695 (mp0) REVERT: X 199 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7821 (mm) REVERT: Z 66 MET cc_start: 0.7430 (mmm) cc_final: 0.7043 (mmm) REVERT: Z 138 LYS cc_start: 0.8161 (ptmt) cc_final: 0.7893 (tttp) REVERT: a 208 TRP cc_start: 0.7207 (t60) cc_final: 0.6509 (t-100) REVERT: b 74 GLU cc_start: 0.7913 (mp0) cc_final: 0.7380 (mp0) REVERT: e 235 ILE cc_start: 0.9000 (mm) cc_final: 0.8736 (mm) REVERT: f 63 PRO cc_start: 0.7067 (Cg_endo) cc_final: 0.6771 (Cg_exo) REVERT: h 198 VAL cc_start: 0.7958 (OUTLIER) cc_final: 0.7739 (p) REVERT: j 129 LYS cc_start: 0.8780 (ptpp) cc_final: 0.8383 (ptpp) REVERT: j 138 LYS cc_start: 0.8216 (ptmt) cc_final: 0.7974 (tttp) REVERT: j 164 ASP cc_start: 0.7803 (p0) cc_final: 0.7481 (p0) REVERT: k 90 ILE cc_start: 0.8891 (mm) cc_final: 0.8644 (mm) REVERT: l 180 ASN cc_start: 0.8526 (t0) cc_final: 0.8224 (t0) REVERT: o 128 ARG cc_start: 0.8216 (tpp80) cc_final: 0.7894 (tpp80) REVERT: o 230 MET cc_start: 0.6851 (tpp) cc_final: 0.6599 (tpp) REVERT: o 235 ILE cc_start: 0.9016 (mm) cc_final: 0.8759 (mm) REVERT: r 177 ASP cc_start: 0.8088 (t0) cc_final: 0.7802 (t70) REVERT: r 179 ASP cc_start: 0.7236 (p0) cc_final: 0.6704 (p0) REVERT: t 184 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.8012 (mt0) REVERT: y 66 MET cc_start: 0.7794 (mmp) cc_final: 0.7190 (mmp) REVERT: z 205 GLN cc_start: 0.7055 (mp10) cc_final: 0.6840 (mp10) outliers start: 266 outliers final: 211 residues processed: 1344 average time/residue: 0.5069 time to fit residues: 1164.4796 Evaluate side-chains 1377 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1160 time to evaluate : 4.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain AA residue 188 VAL Chi-restraints excluded: chain AB residue 188 VAL Chi-restraints excluded: chain AB residue 191 VAL Chi-restraints excluded: chain AC residue 181 ASP Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 2 residue 181 ASP Chi-restraints excluded: chain 2 residue 184 GLU Chi-restraints excluded: chain 3 residue 40 LEU Chi-restraints excluded: chain 3 residue 44 ASN Chi-restraints excluded: chain 3 residue 48 ASN Chi-restraints excluded: chain 3 residue 60 ILE Chi-restraints excluded: chain 3 residue 85 THR Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 3 residue 216 MET Chi-restraints excluded: chain 4 residue 56 LYS Chi-restraints excluded: chain 4 residue 127 THR Chi-restraints excluded: chain 4 residue 147 VAL Chi-restraints excluded: chain 4 residue 175 THR Chi-restraints excluded: chain 4 residue 206 ASP Chi-restraints excluded: chain 4 residue 230 MET Chi-restraints excluded: chain 5 residue 157 THR Chi-restraints excluded: chain 5 residue 192 VAL Chi-restraints excluded: chain 6 residue 179 ASP Chi-restraints excluded: chain 6 residue 180 ASN Chi-restraints excluded: chain 6 residue 188 VAL Chi-restraints excluded: chain 7 residue 181 ASP Chi-restraints excluded: chain 7 residue 184 GLU Chi-restraints excluded: chain 8 residue 44 ASN Chi-restraints excluded: chain 8 residue 46 ASP Chi-restraints excluded: chain 8 residue 81 THR Chi-restraints excluded: chain 8 residue 143 LEU Chi-restraints excluded: chain 8 residue 168 LEU Chi-restraints excluded: chain 8 residue 192 LEU Chi-restraints excluded: chain 8 residue 216 MET Chi-restraints excluded: chain 9 residue 102 VAL Chi-restraints excluded: chain 9 residue 127 THR Chi-restraints excluded: chain 9 residue 175 THR Chi-restraints excluded: chain 9 residue 204 GLU Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain K residue 44 ASN Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 184 GLN Chi-restraints excluded: chain L residue 206 ASP Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain N residue 196 ASP Chi-restraints excluded: chain P residue 44 ASN Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 216 MET Chi-restraints excluded: chain Q residue 48 ASN Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 159 HIS Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 188 VAL Chi-restraints excluded: chain T residue 181 ASP Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 168 LEU Chi-restraints excluded: chain U residue 224 LEU Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 147 VAL Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain W residue 167 ILE Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain X residue 179 ASP Chi-restraints excluded: chain X residue 196 ASP Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Z residue 44 ASN Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 60 ILE Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 117 MET Chi-restraints excluded: chain Z residue 168 LEU Chi-restraints excluded: chain Z residue 188 ASP Chi-restraints excluded: chain Z residue 216 MET Chi-restraints excluded: chain Z residue 220 ASN Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 127 THR Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 206 ASP Chi-restraints excluded: chain b residue 188 VAL Chi-restraints excluded: chain d residue 181 ASP Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 44 ASN Chi-restraints excluded: chain e residue 117 MET Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 188 ASP Chi-restraints excluded: chain e residue 216 MET Chi-restraints excluded: chain f residue 44 ASN Chi-restraints excluded: chain f residue 48 ASN Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 175 THR Chi-restraints excluded: chain f residue 204 GLU Chi-restraints excluded: chain f residue 206 ASP Chi-restraints excluded: chain g residue 157 THR Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain h residue 179 ASP Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain j residue 44 ASN Chi-restraints excluded: chain j residue 46 ASP Chi-restraints excluded: chain j residue 48 ASN Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 163 SER Chi-restraints excluded: chain j residue 168 LEU Chi-restraints excluded: chain j residue 188 ASP Chi-restraints excluded: chain j residue 216 MET Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 127 THR Chi-restraints excluded: chain k residue 173 SER Chi-restraints excluded: chain k residue 188 ASP Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 157 THR Chi-restraints excluded: chain l residue 188 VAL Chi-restraints excluded: chain m residue 179 ASP Chi-restraints excluded: chain m residue 196 ASP Chi-restraints excluded: chain n residue 181 ASP Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 44 ASN Chi-restraints excluded: chain o residue 188 ASP Chi-restraints excluded: chain o residue 224 LEU Chi-restraints excluded: chain p residue 48 ASN Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 173 SER Chi-restraints excluded: chain q residue 73 VAL Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain q residue 191 VAL Chi-restraints excluded: chain t residue 46 ASP Chi-restraints excluded: chain t residue 48 ASN Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 108 LYS Chi-restraints excluded: chain t residue 141 ILE Chi-restraints excluded: chain t residue 168 LEU Chi-restraints excluded: chain t residue 184 GLN Chi-restraints excluded: chain t residue 216 MET Chi-restraints excluded: chain t residue 224 LEU Chi-restraints excluded: chain u residue 127 THR Chi-restraints excluded: chain u residue 175 THR Chi-restraints excluded: chain v residue 73 VAL Chi-restraints excluded: chain v residue 157 THR Chi-restraints excluded: chain w residue 179 ASP Chi-restraints excluded: chain y residue 40 LEU Chi-restraints excluded: chain y residue 44 ASN Chi-restraints excluded: chain y residue 46 ASP Chi-restraints excluded: chain y residue 60 ILE Chi-restraints excluded: chain y residue 117 MET Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 143 LEU Chi-restraints excluded: chain y residue 168 LEU Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 175 THR Chi-restraints excluded: chain z residue 204 GLU Chi-restraints excluded: chain z residue 206 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 689 random chunks: chunk 410 optimal weight: 4.9990 chunk 265 optimal weight: 0.7980 chunk 396 optimal weight: 0.2980 chunk 200 optimal weight: 0.6980 chunk 130 optimal weight: 0.3980 chunk 128 optimal weight: 5.9990 chunk 422 optimal weight: 5.9990 chunk 452 optimal weight: 0.0870 chunk 328 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 521 optimal weight: 1.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 222 GLN ** 4 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 184 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 GLN ** Q 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 144 ASN ** f 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 144 ASN ** k 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 134 GLN z 48 ASN ** z 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 55744 Z= 0.162 Angle : 0.611 11.737 75907 Z= 0.300 Chirality : 0.043 0.283 8515 Planarity : 0.005 0.068 9919 Dihedral : 4.235 46.368 7710 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 3.86 % Allowed : 22.16 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.10), residues: 6968 helix: -0.68 (0.20), residues: 624 sheet: -1.43 (0.11), residues: 2522 loop : -2.39 (0.10), residues: 3822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 180 HIS 0.002 0.000 HIS H 183 PHE 0.014 0.001 PHE K 38 TYR 0.011 0.001 TYR k 190 ARG 0.008 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1401 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1178 time to evaluate : 4.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 180 ASN cc_start: 0.8580 (t0) cc_final: 0.8239 (t0) REVERT: 3 85 THR cc_start: 0.7876 (OUTLIER) cc_final: 0.7575 (t) REVERT: 4 56 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7676 (tptt) REVERT: 9 66 MET cc_start: 0.7125 (mmt) cc_final: 0.6801 (mmt) REVERT: A 138 LYS cc_start: 0.8208 (ptmt) cc_final: 0.7941 (tttp) REVERT: B 66 MET cc_start: 0.6982 (mmt) cc_final: 0.6709 (mmt) REVERT: C 180 ASN cc_start: 0.8640 (t0) cc_final: 0.8326 (t0) REVERT: F 129 LYS cc_start: 0.8806 (ptpp) cc_final: 0.8375 (ptpp) REVERT: G 49 MET cc_start: 0.7449 (ttt) cc_final: 0.7075 (ttt) REVERT: G 66 MET cc_start: 0.7085 (mmt) cc_final: 0.6711 (mmt) REVERT: L 117 MET cc_start: 0.7136 (ptm) cc_final: 0.6887 (ptm) REVERT: L 208 TRP cc_start: 0.7080 (t60) cc_final: 0.6840 (t-100) REVERT: L 216 MET cc_start: 0.7359 (ptm) cc_final: 0.6973 (mtm) REVERT: M 180 ASN cc_start: 0.8446 (t0) cc_final: 0.8039 (t0) REVERT: Q 66 MET cc_start: 0.7092 (mmp) cc_final: 0.6455 (mmp) REVERT: Q 191 GLU cc_start: 0.5793 (tm-30) cc_final: 0.5495 (tm-30) REVERT: Q 208 TRP cc_start: 0.7269 (t60) cc_final: 0.6850 (t-100) REVERT: U 85 THR cc_start: 0.7776 (OUTLIER) cc_final: 0.7563 (t) REVERT: V 208 TRP cc_start: 0.7236 (t60) cc_final: 0.6948 (t-100) REVERT: W 74 GLU cc_start: 0.7990 (mp0) cc_final: 0.7648 (mp0) REVERT: X 199 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7767 (mm) REVERT: Z 66 MET cc_start: 0.7463 (mmm) cc_final: 0.7165 (mmm) REVERT: Z 129 LYS cc_start: 0.8692 (ptpp) cc_final: 0.8467 (ptpp) REVERT: Z 138 LYS cc_start: 0.8155 (ptmt) cc_final: 0.7890 (tttp) REVERT: a 208 TRP cc_start: 0.7215 (t60) cc_final: 0.6559 (t-100) REVERT: b 74 GLU cc_start: 0.7798 (mp0) cc_final: 0.7403 (mp0) REVERT: e 235 ILE cc_start: 0.8983 (mm) cc_final: 0.8717 (mm) REVERT: f 63 PRO cc_start: 0.6908 (Cg_endo) cc_final: 0.6561 (Cg_exo) REVERT: f 66 MET cc_start: 0.7377 (mmt) cc_final: 0.7086 (mmp) REVERT: h 198 VAL cc_start: 0.7930 (OUTLIER) cc_final: 0.7729 (p) REVERT: j 129 LYS cc_start: 0.8776 (ptpp) cc_final: 0.8364 (ptpp) REVERT: j 138 LYS cc_start: 0.8190 (ptmt) cc_final: 0.7958 (tttp) REVERT: j 164 ASP cc_start: 0.7747 (p0) cc_final: 0.7437 (p0) REVERT: k 90 ILE cc_start: 0.8831 (mm) cc_final: 0.8579 (mm) REVERT: l 180 ASN cc_start: 0.8510 (t0) cc_final: 0.8201 (t0) REVERT: o 230 MET cc_start: 0.6906 (tpp) cc_final: 0.6657 (tpp) REVERT: o 235 ILE cc_start: 0.8993 (mm) cc_final: 0.8685 (mm) REVERT: r 177 ASP cc_start: 0.8064 (t0) cc_final: 0.7781 (t70) REVERT: r 179 ASP cc_start: 0.7353 (p0) cc_final: 0.6913 (p0) REVERT: t 184 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7859 (mt0) REVERT: y 129 LYS cc_start: 0.8770 (ptpp) cc_final: 0.8293 (ptpp) REVERT: z 49 MET cc_start: 0.7609 (ttt) cc_final: 0.7162 (ttt) REVERT: z 205 GLN cc_start: 0.7023 (mp10) cc_final: 0.6812 (mp10) outliers start: 223 outliers final: 179 residues processed: 1309 average time/residue: 0.4811 time to fit residues: 1068.9276 Evaluate side-chains 1336 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1151 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain AB residue 188 VAL Chi-restraints excluded: chain AB residue 191 VAL Chi-restraints excluded: chain AB residue 192 VAL Chi-restraints excluded: chain AC residue 181 ASP Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 2 residue 184 GLU Chi-restraints excluded: chain 3 residue 44 ASN Chi-restraints excluded: chain 3 residue 85 THR Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 3 residue 216 MET Chi-restraints excluded: chain 4 residue 56 LYS Chi-restraints excluded: chain 4 residue 127 THR Chi-restraints excluded: chain 4 residue 230 MET Chi-restraints excluded: chain 5 residue 157 THR Chi-restraints excluded: chain 5 residue 192 VAL Chi-restraints excluded: chain 6 residue 180 ASN Chi-restraints excluded: chain 8 residue 44 ASN Chi-restraints excluded: chain 8 residue 81 THR Chi-restraints excluded: chain 8 residue 143 LEU Chi-restraints excluded: chain 9 residue 102 VAL Chi-restraints excluded: chain 9 residue 127 THR Chi-restraints excluded: chain 9 residue 204 GLU Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain K residue 44 ASN Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 184 GLN Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain P residue 44 ASN Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 216 MET Chi-restraints excluded: chain P residue 224 LEU Chi-restraints excluded: chain Q residue 48 ASN Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 188 VAL Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 85 THR Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 168 LEU Chi-restraints excluded: chain U residue 224 LEU Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 147 VAL Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 ASP Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain X residue 179 ASP Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Z residue 44 ASN Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 60 ILE Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 117 MET Chi-restraints excluded: chain Z residue 188 ASP Chi-restraints excluded: chain Z residue 220 ASN Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 127 THR Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 223 THR Chi-restraints excluded: chain b residue 188 VAL Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 44 ASN Chi-restraints excluded: chain e residue 117 MET Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 188 ASP Chi-restraints excluded: chain e residue 216 MET Chi-restraints excluded: chain f residue 44 ASN Chi-restraints excluded: chain f residue 48 ASN Chi-restraints excluded: chain f residue 85 THR Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 204 GLU Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain j residue 44 ASN Chi-restraints excluded: chain j residue 46 ASP Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 163 SER Chi-restraints excluded: chain j residue 188 ASP Chi-restraints excluded: chain j residue 216 MET Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 127 THR Chi-restraints excluded: chain k residue 173 SER Chi-restraints excluded: chain k residue 188 ASP Chi-restraints excluded: chain k residue 206 ASP Chi-restraints excluded: chain k residue 216 MET Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 157 THR Chi-restraints excluded: chain l residue 188 VAL Chi-restraints excluded: chain m residue 196 ASP Chi-restraints excluded: chain n residue 181 ASP Chi-restraints excluded: chain o residue 32 LEU Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 44 ASN Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 168 LEU Chi-restraints excluded: chain o residue 224 LEU Chi-restraints excluded: chain p residue 48 ASN Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 173 SER Chi-restraints excluded: chain p residue 216 MET Chi-restraints excluded: chain q residue 73 VAL Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain q residue 191 VAL Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 141 ILE Chi-restraints excluded: chain t residue 184 GLN Chi-restraints excluded: chain t residue 216 MET Chi-restraints excluded: chain t residue 224 LEU Chi-restraints excluded: chain u residue 85 THR Chi-restraints excluded: chain u residue 127 THR Chi-restraints excluded: chain u residue 175 THR Chi-restraints excluded: chain u residue 206 ASP Chi-restraints excluded: chain v residue 73 VAL Chi-restraints excluded: chain w residue 179 ASP Chi-restraints excluded: chain y residue 40 LEU Chi-restraints excluded: chain y residue 44 ASN Chi-restraints excluded: chain y residue 46 ASP Chi-restraints excluded: chain y residue 60 ILE Chi-restraints excluded: chain y residue 81 THR Chi-restraints excluded: chain y residue 117 MET Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 143 LEU Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 50 ILE Chi-restraints excluded: chain z residue 204 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 689 random chunks: chunk 604 optimal weight: 0.9980 chunk 636 optimal weight: 0.0020 chunk 580 optimal weight: 6.9990 chunk 618 optimal weight: 5.9990 chunk 372 optimal weight: 6.9990 chunk 269 optimal weight: 3.9990 chunk 485 optimal weight: 0.6980 chunk 189 optimal weight: 0.5980 chunk 559 optimal weight: 3.9990 chunk 585 optimal weight: 6.9990 chunk 616 optimal weight: 0.9980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 184 GLN 9 48 ASN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 GLN ** Q 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 144 ASN ** k 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 55744 Z= 0.174 Angle : 0.618 12.633 75907 Z= 0.304 Chirality : 0.043 0.344 8515 Planarity : 0.005 0.069 9919 Dihedral : 4.147 42.686 7703 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 3.64 % Allowed : 22.47 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.10), residues: 6968 helix: -0.58 (0.20), residues: 624 sheet: -1.35 (0.11), residues: 2522 loop : -2.36 (0.10), residues: 3822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP 4 208 HIS 0.002 0.001 HIS v 183 PHE 0.012 0.001 PHE K 38 TYR 0.013 0.001 TYR Z 156 ARG 0.008 0.000 ARG e 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1365 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1155 time to evaluate : 4.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 180 ASN cc_start: 0.8624 (t0) cc_final: 0.8293 (t0) REVERT: 3 85 THR cc_start: 0.7874 (OUTLIER) cc_final: 0.7591 (t) REVERT: 4 56 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7643 (tptt) REVERT: 8 129 LYS cc_start: 0.8811 (ptpp) cc_final: 0.8395 (ptpp) REVERT: A 129 LYS cc_start: 0.8878 (ptpp) cc_final: 0.8605 (ptpp) REVERT: A 138 LYS cc_start: 0.8184 (ptmt) cc_final: 0.7929 (tttp) REVERT: B 66 MET cc_start: 0.6999 (mmt) cc_final: 0.6711 (mmt) REVERT: B 144 ASN cc_start: 0.8798 (t0) cc_final: 0.8525 (t0) REVERT: C 180 ASN cc_start: 0.8626 (t0) cc_final: 0.8310 (t0) REVERT: F 129 LYS cc_start: 0.8805 (ptpp) cc_final: 0.8520 (ptpp) REVERT: G 49 MET cc_start: 0.7449 (ttt) cc_final: 0.7070 (ttt) REVERT: G 66 MET cc_start: 0.7115 (mmt) cc_final: 0.6732 (mmt) REVERT: L 117 MET cc_start: 0.7150 (ptm) cc_final: 0.6883 (ptm) REVERT: L 208 TRP cc_start: 0.7091 (t60) cc_final: 0.6813 (t-100) REVERT: M 180 ASN cc_start: 0.8462 (t0) cc_final: 0.8061 (t0) REVERT: Q 191 GLU cc_start: 0.5806 (tm-30) cc_final: 0.5490 (tm-30) REVERT: Q 208 TRP cc_start: 0.7269 (t60) cc_final: 0.6821 (t-100) REVERT: U 85 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7607 (t) REVERT: V 208 TRP cc_start: 0.7268 (t60) cc_final: 0.6959 (t-100) REVERT: W 74 GLU cc_start: 0.7963 (mp0) cc_final: 0.7624 (mp0) REVERT: X 199 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7786 (mm) REVERT: Z 66 MET cc_start: 0.7440 (mmm) cc_final: 0.7176 (mmm) REVERT: Z 129 LYS cc_start: 0.8716 (ptpp) cc_final: 0.8492 (ptpp) REVERT: Z 138 LYS cc_start: 0.8161 (ptmt) cc_final: 0.7902 (tttp) REVERT: a 208 TRP cc_start: 0.7168 (t60) cc_final: 0.6545 (t-100) REVERT: b 74 GLU cc_start: 0.7824 (mp0) cc_final: 0.7420 (mp0) REVERT: e 235 ILE cc_start: 0.8980 (mm) cc_final: 0.8735 (mm) REVERT: f 66 MET cc_start: 0.7559 (mmt) cc_final: 0.7271 (mmp) REVERT: j 129 LYS cc_start: 0.8797 (ptpp) cc_final: 0.8399 (ptpp) REVERT: j 138 LYS cc_start: 0.8184 (ptmt) cc_final: 0.7965 (tttp) REVERT: j 164 ASP cc_start: 0.7746 (p0) cc_final: 0.7406 (p0) REVERT: k 90 ILE cc_start: 0.8877 (mm) cc_final: 0.8646 (mm) REVERT: l 180 ASN cc_start: 0.8519 (t0) cc_final: 0.8196 (t0) REVERT: o 230 MET cc_start: 0.6975 (tpp) cc_final: 0.6712 (tpp) REVERT: o 235 ILE cc_start: 0.8991 (mm) cc_final: 0.8683 (mm) REVERT: r 177 ASP cc_start: 0.8073 (t0) cc_final: 0.7785 (t70) REVERT: r 179 ASP cc_start: 0.7351 (p0) cc_final: 0.6911 (p0) REVERT: y 120 GLU cc_start: 0.7872 (pm20) cc_final: 0.7624 (pm20) outliers start: 210 outliers final: 181 residues processed: 1286 average time/residue: 0.4893 time to fit residues: 1066.9866 Evaluate side-chains 1330 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1145 time to evaluate : 4.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain AB residue 188 VAL Chi-restraints excluded: chain AB residue 191 VAL Chi-restraints excluded: chain AB residue 192 VAL Chi-restraints excluded: chain AC residue 181 ASP Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 2 residue 184 GLU Chi-restraints excluded: chain 3 residue 60 ILE Chi-restraints excluded: chain 3 residue 85 THR Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 3 residue 216 MET Chi-restraints excluded: chain 4 residue 56 LYS Chi-restraints excluded: chain 4 residue 85 THR Chi-restraints excluded: chain 4 residue 127 THR Chi-restraints excluded: chain 4 residue 147 VAL Chi-restraints excluded: chain 4 residue 175 THR Chi-restraints excluded: chain 4 residue 184 GLN Chi-restraints excluded: chain 4 residue 230 MET Chi-restraints excluded: chain 5 residue 157 THR Chi-restraints excluded: chain 5 residue 192 VAL Chi-restraints excluded: chain 6 residue 180 ASN Chi-restraints excluded: chain 6 residue 188 VAL Chi-restraints excluded: chain 8 residue 44 ASN Chi-restraints excluded: chain 8 residue 81 THR Chi-restraints excluded: chain 9 residue 48 ASN Chi-restraints excluded: chain 9 residue 127 THR Chi-restraints excluded: chain 9 residue 204 GLU Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain K residue 44 ASN Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain P residue 44 ASN Chi-restraints excluded: chain P residue 48 ASN Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 216 MET Chi-restraints excluded: chain P residue 224 LEU Chi-restraints excluded: chain Q residue 48 ASN Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 159 HIS Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 188 VAL Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 85 THR Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 168 LEU Chi-restraints excluded: chain U residue 224 LEU Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 147 VAL Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 ASP Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain X residue 179 ASP Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Z residue 44 ASN Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 60 ILE Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 117 MET Chi-restraints excluded: chain Z residue 188 ASP Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 127 THR Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 184 GLN Chi-restraints excluded: chain a residue 206 ASP Chi-restraints excluded: chain a residue 223 THR Chi-restraints excluded: chain b residue 188 VAL Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 44 ASN Chi-restraints excluded: chain e residue 117 MET Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 188 ASP Chi-restraints excluded: chain e residue 216 MET Chi-restraints excluded: chain f residue 44 ASN Chi-restraints excluded: chain f residue 48 ASN Chi-restraints excluded: chain f residue 85 THR Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 204 GLU Chi-restraints excluded: chain f residue 206 ASP Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain j residue 44 ASN Chi-restraints excluded: chain j residue 46 ASP Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 163 SER Chi-restraints excluded: chain j residue 188 ASP Chi-restraints excluded: chain j residue 216 MET Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 127 THR Chi-restraints excluded: chain k residue 173 SER Chi-restraints excluded: chain k residue 188 ASP Chi-restraints excluded: chain k residue 206 ASP Chi-restraints excluded: chain k residue 216 MET Chi-restraints excluded: chain l residue 188 VAL Chi-restraints excluded: chain n residue 181 ASP Chi-restraints excluded: chain o residue 32 LEU Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 44 ASN Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 168 LEU Chi-restraints excluded: chain o residue 224 LEU Chi-restraints excluded: chain p residue 48 ASN Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 173 SER Chi-restraints excluded: chain p residue 175 THR Chi-restraints excluded: chain p residue 216 MET Chi-restraints excluded: chain q residue 73 VAL Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain q residue 191 VAL Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 141 ILE Chi-restraints excluded: chain t residue 216 MET Chi-restraints excluded: chain t residue 224 LEU Chi-restraints excluded: chain u residue 127 THR Chi-restraints excluded: chain u residue 175 THR Chi-restraints excluded: chain u residue 206 ASP Chi-restraints excluded: chain w residue 179 ASP Chi-restraints excluded: chain w residue 196 ASP Chi-restraints excluded: chain y residue 40 LEU Chi-restraints excluded: chain y residue 44 ASN Chi-restraints excluded: chain y residue 46 ASP Chi-restraints excluded: chain y residue 60 ILE Chi-restraints excluded: chain y residue 81 THR Chi-restraints excluded: chain y residue 117 MET Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 143 LEU Chi-restraints excluded: chain y residue 168 LEU Chi-restraints excluded: chain z residue 50 ILE Chi-restraints excluded: chain z residue 74 THR Chi-restraints excluded: chain z residue 175 THR Chi-restraints excluded: chain z residue 204 GLU Chi-restraints excluded: chain z residue 206 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 689 random chunks: chunk 406 optimal weight: 4.9990 chunk 654 optimal weight: 0.0770 chunk 399 optimal weight: 3.9990 chunk 310 optimal weight: 3.9990 chunk 454 optimal weight: 8.9990 chunk 686 optimal weight: 3.9990 chunk 631 optimal weight: 1.9990 chunk 546 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 422 optimal weight: 6.9990 chunk 335 optimal weight: 1.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 48 ASN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 180 ASN ** i 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.171 55744 Z= 0.252 Angle : 0.734 59.193 75907 Z= 0.391 Chirality : 0.044 0.327 8515 Planarity : 0.005 0.068 9919 Dihedral : 4.158 42.717 7703 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 3.60 % Allowed : 22.33 % Favored : 74.06 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.10), residues: 6968 helix: -0.58 (0.20), residues: 624 sheet: -1.34 (0.11), residues: 2522 loop : -2.36 (0.10), residues: 3822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP 4 208 HIS 0.002 0.001 HIS v 183 PHE 0.028 0.001 PHE T 185 TYR 0.034 0.002 TYR L 190 ARG 0.010 0.000 ARG V 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1354 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1146 time to evaluate : 4.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 180 ASN cc_start: 0.8622 (t0) cc_final: 0.8297 (t0) REVERT: 3 85 THR cc_start: 0.7878 (OUTLIER) cc_final: 0.7651 (m) REVERT: 4 56 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7648 (tptt) REVERT: 9 66 MET cc_start: 0.7157 (mmt) cc_final: 0.6676 (mmt) REVERT: A 129 LYS cc_start: 0.8877 (ptpp) cc_final: 0.8572 (ptpp) REVERT: A 138 LYS cc_start: 0.8188 (ptmt) cc_final: 0.7941 (tttp) REVERT: B 66 MET cc_start: 0.7000 (mmt) cc_final: 0.6716 (mmt) REVERT: B 144 ASN cc_start: 0.8803 (t0) cc_final: 0.8520 (t0) REVERT: C 180 ASN cc_start: 0.8626 (t0) cc_final: 0.8311 (t0) REVERT: F 129 LYS cc_start: 0.8807 (ptpp) cc_final: 0.8523 (ptpp) REVERT: G 49 MET cc_start: 0.7456 (ttt) cc_final: 0.7076 (ttt) REVERT: G 66 MET cc_start: 0.7117 (mmt) cc_final: 0.6739 (mmt) REVERT: L 117 MET cc_start: 0.7160 (ptm) cc_final: 0.6892 (ptm) REVERT: L 208 TRP cc_start: 0.7092 (t60) cc_final: 0.6821 (t-100) REVERT: M 180 ASN cc_start: 0.8478 (t0) cc_final: 0.8062 (t0) REVERT: Q 191 GLU cc_start: 0.5808 (tm-30) cc_final: 0.5496 (tm-30) REVERT: Q 208 TRP cc_start: 0.7272 (t60) cc_final: 0.6823 (t-100) REVERT: U 85 THR cc_start: 0.7818 (OUTLIER) cc_final: 0.7610 (t) REVERT: V 208 TRP cc_start: 0.7211 (t60) cc_final: 0.6946 (t-100) REVERT: W 74 GLU cc_start: 0.7965 (mp0) cc_final: 0.7649 (mp0) REVERT: Z 66 MET cc_start: 0.7450 (mmm) cc_final: 0.7188 (mmm) REVERT: Z 129 LYS cc_start: 0.8716 (ptpp) cc_final: 0.8503 (ptpp) REVERT: Z 138 LYS cc_start: 0.8154 (ptmt) cc_final: 0.7908 (tttp) REVERT: a 208 TRP cc_start: 0.7172 (t60) cc_final: 0.6547 (t-100) REVERT: b 74 GLU cc_start: 0.7829 (mp0) cc_final: 0.7428 (mp0) REVERT: e 235 ILE cc_start: 0.8989 (mm) cc_final: 0.8744 (mm) REVERT: f 66 MET cc_start: 0.7562 (mmt) cc_final: 0.7278 (mmp) REVERT: j 129 LYS cc_start: 0.8798 (ptpp) cc_final: 0.8401 (ptpp) REVERT: j 138 LYS cc_start: 0.8194 (ptmt) cc_final: 0.7981 (tttp) REVERT: j 164 ASP cc_start: 0.7744 (p0) cc_final: 0.7394 (p0) REVERT: k 90 ILE cc_start: 0.8910 (mm) cc_final: 0.8666 (mm) REVERT: l 180 ASN cc_start: 0.8505 (t0) cc_final: 0.8190 (t0) REVERT: o 230 MET cc_start: 0.6979 (tpp) cc_final: 0.6715 (tpp) REVERT: o 235 ILE cc_start: 0.9005 (mm) cc_final: 0.8697 (mm) REVERT: r 177 ASP cc_start: 0.8079 (t0) cc_final: 0.7788 (t70) REVERT: r 179 ASP cc_start: 0.7356 (p0) cc_final: 0.6914 (p0) REVERT: y 120 GLU cc_start: 0.7877 (pm20) cc_final: 0.7656 (pm20) outliers start: 208 outliers final: 201 residues processed: 1272 average time/residue: 0.4888 time to fit residues: 1054.3379 Evaluate side-chains 1348 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1144 time to evaluate : 4.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain AA residue 196 ASP Chi-restraints excluded: chain AB residue 188 VAL Chi-restraints excluded: chain AB residue 191 VAL Chi-restraints excluded: chain AB residue 192 VAL Chi-restraints excluded: chain AC residue 181 ASP Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 2 residue 184 GLU Chi-restraints excluded: chain 3 residue 44 ASN Chi-restraints excluded: chain 3 residue 48 ASN Chi-restraints excluded: chain 3 residue 60 ILE Chi-restraints excluded: chain 3 residue 85 THR Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 3 residue 216 MET Chi-restraints excluded: chain 4 residue 56 LYS Chi-restraints excluded: chain 4 residue 85 THR Chi-restraints excluded: chain 4 residue 127 THR Chi-restraints excluded: chain 4 residue 147 VAL Chi-restraints excluded: chain 4 residue 175 THR Chi-restraints excluded: chain 4 residue 206 ASP Chi-restraints excluded: chain 4 residue 230 MET Chi-restraints excluded: chain 5 residue 157 THR Chi-restraints excluded: chain 5 residue 192 VAL Chi-restraints excluded: chain 6 residue 180 ASN Chi-restraints excluded: chain 6 residue 188 VAL Chi-restraints excluded: chain 7 residue 184 GLU Chi-restraints excluded: chain 8 residue 44 ASN Chi-restraints excluded: chain 8 residue 81 THR Chi-restraints excluded: chain 8 residue 216 MET Chi-restraints excluded: chain 9 residue 127 THR Chi-restraints excluded: chain 9 residue 204 GLU Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain K residue 44 ASN Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain N residue 196 ASP Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain P residue 44 ASN Chi-restraints excluded: chain P residue 48 ASN Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 216 MET Chi-restraints excluded: chain P residue 224 LEU Chi-restraints excluded: chain Q residue 48 ASN Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 159 HIS Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 188 VAL Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 85 THR Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 168 LEU Chi-restraints excluded: chain U residue 224 LEU Chi-restraints excluded: chain V residue 85 THR Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 147 VAL Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 ASP Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain X residue 179 ASP Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Z residue 44 ASN Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 60 ILE Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 117 MET Chi-restraints excluded: chain Z residue 188 ASP Chi-restraints excluded: chain Z residue 216 MET Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 127 THR Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 184 GLN Chi-restraints excluded: chain a residue 206 ASP Chi-restraints excluded: chain a residue 223 THR Chi-restraints excluded: chain b residue 188 VAL Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 44 ASN Chi-restraints excluded: chain e residue 117 MET Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 163 SER Chi-restraints excluded: chain e residue 188 ASP Chi-restraints excluded: chain e residue 216 MET Chi-restraints excluded: chain f residue 44 ASN Chi-restraints excluded: chain f residue 48 ASN Chi-restraints excluded: chain f residue 85 THR Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 174 VAL Chi-restraints excluded: chain f residue 204 GLU Chi-restraints excluded: chain f residue 206 ASP Chi-restraints excluded: chain g residue 157 THR Chi-restraints excluded: chain g residue 180 ASN Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain j residue 44 ASN Chi-restraints excluded: chain j residue 46 ASP Chi-restraints excluded: chain j residue 48 ASN Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 163 SER Chi-restraints excluded: chain j residue 168 LEU Chi-restraints excluded: chain j residue 188 ASP Chi-restraints excluded: chain j residue 216 MET Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 127 THR Chi-restraints excluded: chain k residue 173 SER Chi-restraints excluded: chain k residue 188 ASP Chi-restraints excluded: chain k residue 206 ASP Chi-restraints excluded: chain k residue 216 MET Chi-restraints excluded: chain l residue 188 VAL Chi-restraints excluded: chain n residue 181 ASP Chi-restraints excluded: chain o residue 32 LEU Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 44 ASN Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 168 LEU Chi-restraints excluded: chain o residue 188 ASP Chi-restraints excluded: chain o residue 224 LEU Chi-restraints excluded: chain p residue 48 ASN Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 173 SER Chi-restraints excluded: chain p residue 175 THR Chi-restraints excluded: chain p residue 216 MET Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain q residue 191 VAL Chi-restraints excluded: chain t residue 48 ASN Chi-restraints excluded: chain t residue 85 THR Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 141 ILE Chi-restraints excluded: chain t residue 216 MET Chi-restraints excluded: chain t residue 224 LEU Chi-restraints excluded: chain u residue 85 THR Chi-restraints excluded: chain u residue 127 THR Chi-restraints excluded: chain u residue 175 THR Chi-restraints excluded: chain u residue 206 ASP Chi-restraints excluded: chain v residue 157 THR Chi-restraints excluded: chain w residue 179 ASP Chi-restraints excluded: chain w residue 196 ASP Chi-restraints excluded: chain y residue 40 LEU Chi-restraints excluded: chain y residue 44 ASN Chi-restraints excluded: chain y residue 46 ASP Chi-restraints excluded: chain y residue 60 ILE Chi-restraints excluded: chain y residue 81 THR Chi-restraints excluded: chain y residue 117 MET Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 143 LEU Chi-restraints excluded: chain y residue 168 LEU Chi-restraints excluded: chain z residue 50 ILE Chi-restraints excluded: chain z residue 74 THR Chi-restraints excluded: chain z residue 175 THR Chi-restraints excluded: chain z residue 204 GLU Chi-restraints excluded: chain z residue 206 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 689 random chunks: chunk 434 optimal weight: 0.7980 chunk 582 optimal weight: 8.9990 chunk 167 optimal weight: 0.9980 chunk 503 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 chunk 547 optimal weight: 4.9990 chunk 229 optimal weight: 0.9980 chunk 562 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 100 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 144 ASN ** f 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 184 GLN ** z 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.110186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.099053 restraints weight = 116578.399| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.09 r_work: 0.3452 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.240 55744 Z= 0.249 Angle : 0.770 59.199 75907 Z= 0.419 Chirality : 0.044 0.482 8515 Planarity : 0.005 0.069 9919 Dihedral : 4.155 42.749 7703 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.64 % Favored : 90.34 % Rotamer: Outliers : 3.50 % Allowed : 22.44 % Favored : 74.06 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.10), residues: 6968 helix: -0.58 (0.20), residues: 624 sheet: -1.34 (0.11), residues: 2522 loop : -2.36 (0.10), residues: 3822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP 4 208 HIS 0.002 0.001 HIS v 183 PHE 0.028 0.001 PHE T 185 TYR 0.027 0.001 TYR B 190 ARG 0.010 0.000 ARG V 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15587.25 seconds wall clock time: 271 minutes 34.30 seconds (16294.30 seconds total)